diff --git a/src/main/pane-hosts.ts b/src/main/pane-hosts.ts
index 9bfd0a4..9c5a047 100644
--- a/src/main/pane-hosts.ts
+++ b/src/main/pane-hosts.ts
@@ -83,6 +83,17 @@ function persist(paneId: string, patch: SavedPaneWindow): void {
     }
 }
 
+// Everything we remember about a pane window, read in one place so the debounced
+// save, the flush-on-close and the flush-on-quit can never disagree about what
+// "remembered" means. alwaysOnTop is in here because it was being RESTORED and never
+// written — a setting that could only ever be turned on by hand-editing the config.
+function snapshot(win: BrowserWindow): SavedPaneWindow {
+    return {
+        bounds: { ...win.getNormalBounds(), maximized: false },
+        alwaysOnTop: win.isAlwaysOnTop(),
+    };
+}
+
 // setDesktopConfig is writeFileSync + renameSync. Wiring that straight to 'moved'
 // and 'resized' means a synchronous disk write for every frame of a drag — on
 // macOS, dozens per second, in the main process, where they block everything else.
@@ -107,7 +118,7 @@ function flushGeometry(win: BrowserWindow, paneId: string): void {
     const timer = saveTimers.get(paneId);
     if (timer) { clearTimeout(timer); saveTimers.delete(paneId); }
     if (win.isDestroyed()) return;
-    persist(paneId, { bounds: { ...win.getNormalBounds(), maximized: false } });
+    persist(paneId, snapshot(win));
 }
 
 // ── Adoption ────────────────────────────────────────────────────────────────
@@ -146,8 +157,7 @@ export function adoptPaneWindow(win: BrowserWindow, paneId: string): void {
     // in a crash, and the whole point of remembering geometry is that you never
     // place it twice.
     const save = (): void => {
-        persistSoon(paneId, () =>
-            win.isDestroyed() ? null : { bounds: { ...win.getNormalBounds(), maximized: false } });
+        persistSoon(paneId, () => (win.isDestroyed() ? null : snapshot(win)));
     };
     win.on('moved', save);
     win.on('resized', save);
@@ -178,6 +188,11 @@ export function adoptPaneWindow(win: BrowserWindow, paneId: string): void {
 }
 
 export function closeAllPanes(): void {
+    // destroy() does NOT fire 'close', so the flush wired to that event never runs on
+    // this path — and the debounced save may still be pending. Move a pane, quit two
+    // seconds later, and its position would be gone. Flush every pane first.
+    windows.forEach((win, paneId) => flushGeometry(win, paneId));
+
     // Called when the main window goes. A pane window holds a DOM node belonging to
     // the main window's document — with the main window gone there is nothing left
     // to dock it back into. And worse: a pane HIDDEN in the tray is still an open
diff --git a/src/main/pane-tray.ts b/src/main/pane-tray.ts
index 229d176..5804b22 100644
--- a/src/main/pane-tray.ts
+++ b/src/main/pane-tray.ts
@@ -47,10 +47,13 @@ let panes: TrayPane[] = [];
 let actions: TrayPaneActions | null = null;
 
 function iconPath(): string {
-    // Windows wants an .ico; macOS and Linux take a PNG. macOS additionally wants
-    // a monochrome template image, which the 16px PNG is not — so it will render
-    // in colour there. Acceptable, and preferable to shipping no tray at all;
-    // a proper …Template.png is a follow-up.
+    // Windows wants an .ico; macOS and Linux take a PNG. build:ts copies
+    // resources/icons/icon.ico -> tray.ico and resources/icons/32x32.png -> tray.png.
+    //
+    // macOS additionally wants a monochrome TEMPLATE image, which a 32px colour PNG
+    // is not — so the tray icon will render in colour there rather than adapting to
+    // light/dark menu bars. Acceptable, and far preferable to shipping no tray at
+    // all; a proper …Template.png is a follow-up.
     return path.join(__dirname, process.platform === 'win32' ? 'tray.ico' : 'tray.png');
 }
 
diff --git a/tests/window-bounds.test.js b/tests/window-bounds.test.js
index bac83af..035b431 100644
--- a/tests/window-bounds.test.js
+++ b/tests/window-bounds.test.js
@@ -57,3 +57,41 @@ test('fractional coordinates are rounded to integers', () => {
     const out = sanitizeWindowBounds({ x: 10.6, y: 20.4, width: 1200.5, height: 800.2 }, [PRIMARY]);
     assert.deepEqual(out, { x: 11, y: 20, width: 1201, height: 800, maximized: false });
 });
+
+// ── Custom sizing (pane windows) ────────────────────────────────────────────
+//
+// sanitizeWindowBounds grew a `sizing` parameter so pane pop-outs could be small.
+// Without it, a 380×560 pane restored through the MAIN window's 800×600 floor would
+// be silently inflated to 800×600 — three times the size the plugin asked for. The
+// default argument keeps every existing call site byte-for-byte identical, so these
+// tests exist to pin the override itself, which is the part nothing else covers.
+
+const PANE_SIZING = { minWidth: 240, minHeight: 180, defaultWidth: 380, defaultHeight: 560 };
+
+test('custom sizing: a small pane is NOT inflated to the main window floor', () => {
+    const out = sanitizeWindowBounds({ x: 100, y: 100, width: 380, height: 560 }, [PRIMARY], PANE_SIZING);
+    assert.deepEqual(out, { x: 100, y: 100, width: 380, height: 560, maximized: false });
+});
+
+test('custom sizing: the min clamp uses the override, not MIN_WIDTH/MIN_HEIGHT', () => {
+    // Below the pane minimum (240×180) — clamped up to it, and nowhere near 800×600.
+    const out = sanitizeWindowBounds({ x: 10, y: 10, width: 50, height: 20 }, [PRIMARY], PANE_SIZING);
+    assert.deepEqual(out, { x: 10, y: 10, width: 240, height: 180, maximized: false });
+});
+
+test('custom sizing: missing/corrupt bounds fall back to the override defaults', () => {
+    assert.deepEqual(
+        sanitizeWindowBounds(undefined, [PRIMARY], PANE_SIZING),
+        { width: 380, height: 560, maximized: false },
+    );
+    assert.deepEqual(
+        sanitizeWindowBounds({ x: 'nope', y: 0, width: 380, height: 560 }, [PRIMARY], PANE_SIZING),
+        { width: 380, height: 560, maximized: false },
+    );
+});
+
+test('omitting sizing keeps the main window behaviour exactly as before', () => {
+    // The whole point of the default argument: existing call sites must not shift.
+    const out = sanitizeWindowBounds({ x: 10, y: 10, width: 50, height: 20 }, [PRIMARY]);
+    assert.deepEqual(out, { x: 10, y: 10, width: MIN_WIDTH, height: MIN_HEIGHT, maximized: false });
+});