diff --git a/src/layoutmanager.js b/src/layoutmanager.js
index 87884fd..7ab1e91 100644
--- a/src/layoutmanager.js
+++ b/src/layoutmanager.js
@@ -104,7 +104,48 @@ function createPlaceholderPane(paneName) {
  * @returns {Object} Layout definition object
  */
 export function serializeLayout(rootElement) {
-  const layoutNode = serializeLayoutNode(rootElement.firstChild);
+  if (!rootElement.firstChild) {
+    throw new Error("No layout to serialize");
+  }
+
+  console.log('[serializeLayout] rootElement has', rootElement.children.length, 'children:');
+  for (let i = 0; i < rootElement.children.length; i++) {
+    console.log(`  [${i}]:`, rootElement.children[i].className);
+  }
+
+  let layoutNode;
+
+  // Check if rootElement itself acts as a grid (has 2 children from a split)
+  if (rootElement.children.length === 2) {
+    // rootElement is acting as a grid container
+    // Check if it has grid attributes
+    const isHorizontal = rootElement.classList.contains("horizontal-grid");
+    const isVertical = rootElement.classList.contains("vertical-grid");
+    const percent = parseFloat(rootElement.getAttribute("lb-percent")) || 50;
+
+    if (isHorizontal || isVertical) {
+      console.log('[serializeLayout] rootElement is a grid, serializing both children');
+      layoutNode = {
+        type: isHorizontal ? "horizontal-grid" : "vertical-grid",
+        percent: percent,
+        children: [
+          serializeLayoutNode(rootElement.children[0]),
+          serializeLayoutNode(rootElement.children[1])
+        ]
+      };
+    } else {
+      // No grid classes, but has 2 children - this shouldn't happen but handle it
+      console.warn('[serializeLayout] rootElement has 2 children but no grid classes, serializing first child only');
+      layoutNode = serializeLayoutNode(rootElement.firstChild);
+    }
+  } else {
+    // Single child, serialize it directly
+    console.log('[serializeLayout] Starting from element:', rootElement.firstChild.className);
+    layoutNode = serializeLayoutNode(rootElement.firstChild);
+  }
+
+  console.log('[serializeLayout] Serialized layout:', JSON.stringify(layoutNode, null, 2));
+
   return {
     name: "Custom Layout",
     description: "User-created layout",
@@ -116,26 +157,39 @@ export function serializeLayout(rootElement) {
  * Recursively serializes a layout node
  * @private
  */
-function serializeLayoutNode(element) {
+function serializeLayoutNode(element, depth = 0) {
+  const indent = '  '.repeat(depth);
+  console.log(`${indent}[serializeLayoutNode depth=${depth}] element:`, element.className, 'children:', element.children.length);
+
   if (!element) {
     throw new Error("Cannot serialize null element");
   }
 
-  // Check if this is a pane
-  if (element.classList.contains("pane") && !element.classList.contains("horizontal-grid") && !element.classList.contains("vertical-grid")) {
-    // Extract pane name from the element (stored in data attribute or class)
-    const paneName = element.getAttribute("data-pane-name") || "stage";
+  // Check if this is a pane (has data-pane-name attribute)
+  // This check must come first, as panes may also have grid classes for internal layout
+  if (element.hasAttribute("data-pane-name")) {
+    // The data-pane-name is kebab-case, but we need to save the camelCase key
+    // that matches the panes object keys, not the name property
+    const dataName = element.getAttribute("data-pane-name");
+
+    // Convert kebab-case to camelCase (e.g., "timeline-v2" -> "timelineV2")
+    const camelCaseName = dataName.replace(/-([a-z0-9])/g, (g) => g[1].toUpperCase());
+
+    console.log(`${indent}  -> Found pane: ${camelCaseName}`);
+
     return {
       type: "pane",
-      name: paneName
+      name: camelCaseName
     };
   }
 
-  // Check if this is a grid
+  // Check if this is a grid (split pane structure)
   if (element.classList.contains("horizontal-grid") || element.classList.contains("vertical-grid")) {
     const isHorizontal = element.classList.contains("horizontal-grid");
     const percent = parseFloat(element.getAttribute("lb-percent")) || 50;
 
+    console.log(`${indent}  -> Found ${isHorizontal ? 'horizontal' : 'vertical'} grid with ${percent}% split`);
+
     if (element.children.length !== 2) {
       throw new Error("Grid must have exactly 2 children");
     }
@@ -144,15 +198,24 @@ function serializeLayoutNode(element) {
       type: isHorizontal ? "horizontal-grid" : "vertical-grid",
       percent: percent,
       children: [
-        serializeLayoutNode(element.children[0]),
-        serializeLayoutNode(element.children[1])
+        serializeLayoutNode(element.children[0], depth + 1),
+        serializeLayoutNode(element.children[1], depth + 1)
       ]
     };
   }
 
+  // Check if this is a panecontainer wrapper - recurse into it
+  if (element.classList.contains("panecontainer")) {
+    console.log(`${indent}  -> Found panecontainer, recursing into child`);
+    if (element.children.length === 1) {
+      return serializeLayoutNode(element.children[0], depth);
+    }
+  }
+
   // If element has only one child, recurse into it
   if (element.children.length === 1) {
-    return serializeLayoutNode(element.children[0]);
+    console.log(`${indent}  -> Element has 1 child, recursing`);
+    return serializeLayoutNode(element.children[0], depth);
   }
 
   throw new Error(`Cannot serialize element: ${element.className}`);
diff --git a/src/main.js b/src/main.js
index f5b8608..cebda20 100644
--- a/src/main.js
+++ b/src/main.js
@@ -112,7 +112,7 @@ import { actions, initializeActions, updateAutomationName } from "./actions/inde
 
 // Layout system
 import { defaultLayouts, getLayout, getLayoutNames } from "./layouts.js";
-import { buildLayout, loadLayoutByKeyOrName, saveCustomLayout } from "./layoutmanager.js";
+import { buildLayout, loadLayoutByKeyOrName, saveCustomLayout, serializeLayout } from "./layoutmanager.js";
 
 const {
   writeTextFile: writeTextFile,
@@ -1669,11 +1669,15 @@ async function _save(path) {
       }
     }
 
+    // Serialize current layout structure (panes, splits, sizes)
+    const serializedLayout = serializeLayout(rootPane);
+
     const fileData = {
       version: "2.0.0",
       width: config.fileWidth,
       height: config.fileHeight,
       fps: config.framerate,
+      layoutState: serializedLayout, // Save current layout structure
       actions: undoStack,
       json: root.toJSON(),
       // Audio pool at the end for human readability
@@ -2094,6 +2098,37 @@ async function _open(path, returnJson = false) {
             context.activeObject.activeLayer = context.activeObject.layers[0];
           }
 
+          // Restore layout if saved and preference is enabled
+          console.log('[JS] Layout restoration check:', {
+            restoreLayoutFromFile: config.restoreLayoutFromFile,
+            hasLayoutState: !!file.layoutState,
+            layoutState: file.layoutState
+          });
+
+          if (config.restoreLayoutFromFile && file.layoutState) {
+            try {
+              console.log('[JS] Restoring saved layout:', file.layoutState);
+              // Clear existing layout
+              while (rootPane.firstChild) {
+                rootPane.removeChild(rootPane.firstChild);
+              }
+              layoutElements.length = 0;
+              canvases.length = 0;
+
+              // Build layout from saved state
+              buildLayout(rootPane, file.layoutState, panes, createPane, splitPane);
+
+              // Update UI after layout change
+              updateAll();
+              updateUI();
+              console.log('[JS] Layout restored successfully');
+            } catch (error) {
+              console.error('[JS] Failed to restore layout, using default:', error);
+            }
+          } else {
+            console.log('[JS] Skipping layout restoration');
+          }
+
           // Restore audio tracks and clips to the Rust backend
           // The fromJSON method only creates JavaScript objects,
           // but doesn't initialize them in the audio engine
@@ -4994,15 +5029,25 @@ async function startup() {
     }
   });
 
+  console.log('[startup] window.openedFiles:', window.openedFiles);
+  console.log('[startup] config.reopenLastSession:', config.reopenLastSession);
+  console.log('[startup] config.recentFiles:', config.recentFiles);
+
+  // Always update start screen data so it's ready when needed
+  await updateStartScreen(config);
+
   if (!window.openedFiles?.length) {
     if (config.reopenLastSession && config.recentFiles?.length) {
+      console.log('[startup] Reopening last session:', config.recentFiles[0]);
       document.body.style.cursor = "wait"
       setTimeout(()=>_open(config.recentFiles[0]), 10)
     } else {
-      // Show start screen instead of new file dialog
-      await updateStartScreen(config);
+      console.log('[startup] Showing start screen');
+      // Show start screen
       showStartScreen();
     }
+  } else {
+    console.log('[startup] Files already opened, skipping start screen');
   }
 }
 
@@ -6441,6 +6486,11 @@ async function renderMenu() {
         action: actions.selectNone.create,
         accelerator: getShortcut("selectNone"),
       },
+      {
+        text: "Preferences",
+        enabled: true,
+        action: showPreferencesDialog,
+      },
     ],
   });
 
@@ -10231,6 +10281,100 @@ function showSavePresetDialog(container) {
   });
 }
 
+// Show preferences dialog
+function showPreferencesDialog() {
+  const dialog = document.createElement('div');
+  dialog.className = 'modal-overlay';
+  dialog.innerHTML = `
+    <div class="modal-dialog preferences-dialog">
+      <h3>Preferences</h3>
+      <form id="preferences-form">
+        <div class="form-group">
+          <label>Default BPM</label>
+          <input type="number" id="pref-bpm" min="20" max="300" value="${config.bpm}" />
+        </div>
+        <div class="form-group">
+          <label>Default Framerate</label>
+          <input type="number" id="pref-framerate" min="1" max="120" value="${config.framerate}" />
+        </div>
+        <div class="form-group">
+          <label>Default File Width</label>
+          <input type="number" id="pref-width" min="100" max="10000" value="${config.fileWidth}" />
+        </div>
+        <div class="form-group">
+          <label>Default File Height</label>
+          <input type="number" id="pref-height" min="100" max="10000" value="${config.fileHeight}" />
+        </div>
+        <div class="form-group">
+          <label>Scroll Speed</label>
+          <input type="number" id="pref-scroll-speed" min="0.1" max="10" step="0.1" value="${config.scrollSpeed}" />
+        </div>
+        <div class="form-group">
+          <label>
+            <input type="checkbox" id="pref-reopen-session" ${config.reopenLastSession ? 'checked' : ''} />
+            Reopen last session on startup
+          </label>
+        </div>
+        <div class="form-group">
+          <label>
+            <input type="checkbox" id="pref-restore-layout" ${config.restoreLayoutFromFile ? 'checked' : ''} />
+            Restore layout when opening files
+          </label>
+        </div>
+        <div class="form-group">
+          <label>
+            <input type="checkbox" id="pref-debug" ${config.debug ? 'checked' : ''} />
+            Enable debug mode
+          </label>
+        </div>
+        <div class="form-actions">
+          <button type="button" class="btn-cancel">Cancel</button>
+          <button type="submit" class="btn-primary">Save</button>
+        </div>
+      </form>
+    </div>
+  `;
+
+  document.body.appendChild(dialog);
+
+  // Focus first input
+  setTimeout(() => dialog.querySelector('#pref-bpm')?.focus(), 100);
+
+  // Handle cancel
+  dialog.querySelector('.btn-cancel').addEventListener('click', () => {
+    dialog.remove();
+  });
+
+  // Handle save
+  dialog.querySelector('#preferences-form').addEventListener('submit', async (e) => {
+    e.preventDefault();
+
+    // Update config values
+    config.bpm = parseInt(dialog.querySelector('#pref-bpm').value);
+    config.framerate = parseInt(dialog.querySelector('#pref-framerate').value);
+    config.fileWidth = parseInt(dialog.querySelector('#pref-width').value);
+    config.fileHeight = parseInt(dialog.querySelector('#pref-height').value);
+    config.scrollSpeed = parseFloat(dialog.querySelector('#pref-scroll-speed').value);
+    config.reopenLastSession = dialog.querySelector('#pref-reopen-session').checked;
+    config.restoreLayoutFromFile = dialog.querySelector('#pref-restore-layout').checked;
+    config.debug = dialog.querySelector('#pref-debug').checked;
+
+    // Save config to localStorage
+    await saveConfig();
+
+    dialog.remove();
+
+    console.log('Preferences saved:', config);
+  });
+
+  // Close on background click
+  dialog.addEventListener('click', (e) => {
+    if (e.target === dialog) {
+      dialog.remove();
+    }
+  });
+}
+
 // Helper function to convert MIDI note number to note name
 function midiToNoteName(midiNote) {
   const noteNames = ['C', 'C#', 'D', 'D#', 'E', 'F', 'F#', 'G', 'G#', 'A', 'A#', 'B'];
diff --git a/src/startscreen.js b/src/startscreen.js
index f35e939..8d5ffdb 100644
--- a/src/startscreen.js
+++ b/src/startscreen.js
@@ -14,6 +14,7 @@ export function createStartScreen(callback) {
     startScreenContainer = document.createElement('div');
     startScreenContainer.id = 'startScreen';
     startScreenContainer.className = 'start-screen';
+    startScreenContainer.style.display = 'none'; // Hidden by default
 
     // Create welcome title
     const title = document.createElement('h1');
@@ -170,6 +171,8 @@ function createFocusCard(focus) {
 export async function updateStartScreen(config) {
     if (!startScreenContainer) return;
 
+    console.log('[updateStartScreen] config.recentFiles:', config.recentFiles);
+
     // Update last session
     const lastSessionDiv = document.getElementById('lastSessionFile');
     if (lastSessionDiv) {
diff --git a/src/state.js b/src/state.js
index 112fb94..0e05465 100644
--- a/src/state.js
+++ b/src/state.js
@@ -125,9 +125,27 @@ export async function loadConfig() {
     // Merge loaded config with defaults
     Object.assign(config, deepMerge({ ...config }, loaded));
 
+    // Ensure recentFiles is always an array (fix legacy string format)
+    let needsResave = false;
+    if (typeof config.recentFiles === 'string') {
+      config.recentFiles = config.recentFiles.split(',').filter(f => f.length > 0);
+      needsResave = true;
+    } else if (!Array.isArray(config.recentFiles)) {
+      config.recentFiles = [];
+      needsResave = true;
+    }
+
     // Make config accessible to widgets via context
     context.config = config;
 
+    console.log('[loadConfig] Loaded config.recentFiles:', config.recentFiles);
+
+    // Re-save config if we had to fix the format
+    if (needsResave) {
+      console.log('[loadConfig] Re-saving config to fix array format');
+      await saveConfig();
+    }
+
     return config;
   } catch (error) {
     console.log("Error loading config, using defaults:", error);
@@ -154,6 +172,7 @@ export async function addRecentFile(filePath) {
     filePath,
     ...config.recentFiles.filter(file => file !== filePath)
   ].slice(0, 10);
+  console.log('[addRecentFile] Added file, recentFiles now:', config.recentFiles);
   await saveConfig();
 }
 
diff --git a/src/styles.css b/src/styles.css
index bb5b90d..b31d04d 100644
--- a/src/styles.css
+++ b/src/styles.css
@@ -1992,7 +1992,8 @@ button {
   font-weight: 500;
 }
 
-.form-group input,
+.form-group input[type="text"],
+.form-group input[type="number"],
 .form-group textarea {
   width: 100%;
   background: #1e1e1e;
@@ -2005,6 +2006,19 @@ button {
   box-sizing: border-box;
 }
 
+.form-group input[type="checkbox"] {
+  width: auto;
+  margin-right: 8px;
+  cursor: pointer;
+}
+
+.form-group label:has(input[type="checkbox"]) {
+  display: flex;
+  align-items: center;
+  cursor: pointer;
+  color: #ddd;
+}
+
 .form-group input:focus,
 .form-group textarea:focus {
   outline: none;
@@ -2219,7 +2233,7 @@ button {
   font-size: 1.1em;
   padding: 12px;
   background: var(--surface-light);
-  border: 1px solid var(--border-light);
+  border: 1px solid var(--shadow);
   border-radius: 8px;
   box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1);
   transition: all 0.2s;
@@ -2267,7 +2281,7 @@ button {
   width: 180px;
   padding: 24px;
   background: var(--surface-light);
-  border: 2px solid var(--border-light);
+  border: 2px solid var(--shadow);
   border-radius: 12px;
   box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1);
   cursor: pointer;
@@ -2290,7 +2304,7 @@ button {
   display: flex;
   align-items: center;
   justify-content: center;
-  border: 3px solid var(--button-hover);
+  border: 3px solid var(--shadow);
   border-radius: 8px;
   background: var(--surface);
 }