diff --git a/apps/desktop/e2e/send-message.spec.ts b/apps/desktop/e2e/send-message.spec.ts
index 4220c79791..10f483a161 100644
--- a/apps/desktop/e2e/send-message.spec.ts
+++ b/apps/desktop/e2e/send-message.spec.ts
@@ -83,22 +83,33 @@ test('renders a settled Mermaid fence as a diagram', async ({ window: page }) =>
   await expect(diagram.locator('.maka-mermaid-source')).toContainText('flowchart TB');
   await viewSource.click();
 
-  const toolbar = diagram.locator('.maka-mermaid-toolbar');
-  const toolbarBeforeZoom = await toolbar.boundingBox();
-  const diagramBeforeZoom = await diagram.boundingBox();
-  const viewportHeightBeforeZoom = await viewport.evaluate((element) => element.getBoundingClientRect().height);
+  // Zoom moves the diagram's content, never its chrome. Read the toolbar
+  // offset and the viewport height inside one evaluate: the transcript is a
+  // bottom-pinned scroller that re-pins on every ResizeObserver update, so two
+  // separate boundingBox() round-trips sample the same element at two scroll
+  // positions and turn that drift into a phantom offset change (#2000).
+  const readChrome = () => diagram.evaluate((element) => {
+    const diagramTop = element.getBoundingClientRect().top;
+    const toolbarTop = element.querySelector('.maka-mermaid-toolbar')?.getBoundingClientRect().top;
+    const viewportHeight = element.querySelector('.maka-mermaid-viewport')?.getBoundingClientRect().height;
+    return { toolbarOffset: (toolbarTop ?? 0) - diagramTop, viewportHeight: viewportHeight ?? 0 };
+  });
+  const chromeBeforeZoom = await readChrome();
   const zoomIn = diagram.getByRole('button', { name: '放大图表' });
   await zoomIn.click();
   await expect(diagram).toHaveAttribute('data-maka-mermaid-zoom', '1.25');
   await zoomIn.click();
   await expect(diagram).toHaveAttribute('data-maka-mermaid-zoom', '1.50');
-  const toolbarAfterZoom = await toolbar.boundingBox();
-  const diagramAfterZoom = await diagram.boundingBox();
-  const viewportHeightAfterZoom = await viewport.evaluate((element) => element.getBoundingClientRect().height);
-  const toolbarOffsetBeforeZoom = (toolbarBeforeZoom?.y ?? 0) - (diagramBeforeZoom?.y ?? 0);
-  const toolbarOffsetAfterZoom = (toolbarAfterZoom?.y ?? 0) - (diagramAfterZoom?.y ?? 0);
-  expect(Math.abs(toolbarOffsetAfterZoom - toolbarOffsetBeforeZoom)).toBeLessThanOrEqual(1);
-  expect(Math.abs(viewportHeightAfterZoom - viewportHeightBeforeZoom)).toBeLessThanOrEqual(1);
+  // Poll for the steady state: the zoomed layout settles over a rAF, a
+  // ResizeObserver pass, and the scroller's re-pin, so a single instantaneous
+  // read asserts a frame the user never sees.
+  await expect.poll(async () => {
+    const chrome = await readChrome();
+    return Math.max(
+      Math.abs(chrome.toolbarOffset - chromeBeforeZoom.toolbarOffset),
+      Math.abs(chrome.viewportHeight - chromeBeforeZoom.viewportHeight),
+    );
+  }).toBeLessThanOrEqual(1);
   await expect.poll(() => viewport.evaluate((element) =>
     element.scrollWidth > element.clientWidth || element.scrollHeight > element.clientHeight)).toBe(true);
   const zoomedBounds = await diagram.evaluate((element) => {
diff --git a/packages/headless/src/__tests__/harbor-cell.test.ts b/packages/headless/src/__tests__/harbor-cell.test.ts
index a51f76b8b3..c23166a0a0 100644
--- a/packages/headless/src/__tests__/harbor-cell.test.ts
+++ b/packages/headless/src/__tests__/harbor-cell.test.ts
@@ -1216,9 +1216,19 @@ describe('runHarborCell', () => {
       const fallback = new Promise<IsolatedCommandResult>((resolve) => {
         releaseFallback = () => resolve({ exitCode: 0, stdout: '', stderr: '' });
       });
-      const fallbackTimer = setTimeout(releaseFallback, 5_000);
+      // The deadline is a wall-clock timer started when the cell is set up, so
+      // it races the cell's own storage/session/first-send cost before the turn
+      // ever reaches the tool. Lose that race and the run is still cancelled by
+      // `benchmark.deadline` while the backend is never stopped — the empty
+      // `stopModes` seen in CI. Budget the setup generously and name the race,
+      // so a future loss reports itself instead of a bare deepEqual mismatch.
+      const settleAfterMs = 3_000;
+      const startedAt = Date.now();
+      let toolActiveAfterMs: number | undefined;
+      const fallbackTimer = setTimeout(releaseFallback, settleAfterMs + 5_000);
       const executor: IsolatedToolExecutor = {
         exec: async (_input, control) => {
+          toolActiveAfterMs ??= Date.now() - startedAt;
           const signal = control?.abortSignal;
           if (!signal) return await fallback;
           return await new Promise<IsolatedCommandResult>((_resolve, reject) => {
@@ -1233,7 +1243,7 @@ describe('runHarborCell', () => {
           cwd: workspaceDir,
           outputDir,
           storageRoot,
-          settleAfterMs: 1_000,
+          settleAfterMs,
           realBackendIsolation: {
             kind: 'external',
             label: 'cancellable test executor',
@@ -1247,11 +1257,17 @@ describe('runHarborCell', () => {
             });
           },
         }),
-        3_000,
+        settleAfterMs + 10_000,
         'Harbor cell did not cancel its active isolated tool',
       );
       clearTimeout(fallbackTimer);
 
+      assert.ok(
+        toolActiveAfterMs !== undefined && toolActiveAfterMs < settleAfterMs,
+        toolActiveAfterMs === undefined
+          ? `the isolated tool must be active when the deadline fires, but it never started within the ${settleAfterMs}ms budget`
+          : `the isolated tool must be active when the deadline fires, but it started ${toolActiveAfterMs}ms in, past the ${settleAfterMs}ms budget`,
+      );
       assert.equal(result.settledByDeadline, true);
       assert.deepEqual(backend?.stopModes, ['immediate']);
       assert.equal(result.output.tokenSummary?.total, 18);
diff --git a/packages/ui/src/plan-reminder-form-dialog.tsx b/packages/ui/src/plan-reminder-form-dialog.tsx
index 7aa0dfedf1..0e81acdcfc 100644
--- a/packages/ui/src/plan-reminder-form-dialog.tsx
+++ b/packages/ui/src/plan-reminder-form-dialog.tsx
@@ -252,7 +252,12 @@ export function PlanReminderFormDialog(props: {
               id="maka-plan-title"
               className="maka-plan-title-input"
               value={title}
-              autoFocus
+              // Not React's `autoFocus`: it runs during commit, before the
+              // dialog's showModal() makes the field visible, so the focus
+              // silently fails. Astryx's Dialog focuses `[data-autofocus]`
+              // after opening — the same seam TextInput's `hasAutoFocus`
+              // emits, which this bare input replaced.
+              data-autofocus
               onChange={(event) => {
                 setTitleTouched(true);
                 setTitle(event.target.value.slice(0, 120));