diff --git a/packages/cli/src/ui/components/messages/ToolShared.tsx b/packages/cli/src/ui/components/messages/ToolShared.tsx
index 0ff984d7cbe..fc1dc6e45a6 100644
--- a/packages/cli/src/ui/components/messages/ToolShared.tsx
+++ b/packages/cli/src/ui/components/messages/ToolShared.tsx
@@ -80,20 +80,24 @@ export function useFocusHint(
   isThisShellFocused: boolean,
   resultDisplay: ToolResultDisplay | undefined,
 ) {
-  const [lastUpdateTime, setLastUpdateTime] = useState<Date | null>(null);
   const [userHasFocused, setUserHasFocused] = useState(false);
+
+  // Derive a stable reset key for the inactivity timer. For strings and arrays
+  // (shell output), we use the length to capture updates without referential
+  // identity issues or expensive deep comparisons.
+  const resetKey =
+    typeof resultDisplay === 'string'
+      ? resultDisplay.length
+      : Array.isArray(resultDisplay)
+        ? resultDisplay.length
+        : !!resultDisplay;
+
   const showFocusHint = useInactivityTimer(
     isThisShellFocusable,
-    lastUpdateTime ? lastUpdateTime.getTime() : 0,
+    resetKey,
     SHELL_FOCUS_HINT_DELAY_MS,
   );
 
-  useEffect(() => {
-    if (resultDisplay) {
-      setLastUpdateTime(new Date());
-    }
-  }, [resultDisplay]);
-
   useEffect(() => {
     if (isThisShellFocused) {
       setUserHasFocused(true);
diff --git a/packages/cli/src/ui/hooks/useConsoleMessages.test.tsx b/packages/cli/src/ui/hooks/useConsoleMessages.test.tsx
index 466c5966844..8761ef7167f 100644
--- a/packages/cli/src/ui/hooks/useConsoleMessages.test.tsx
+++ b/packages/cli/src/ui/hooks/useConsoleMessages.test.tsx
@@ -96,7 +96,7 @@ describe('useConsoleMessages', () => {
     });
 
     await act(async () => {
-      await vi.advanceTimersByTimeAsync(20);
+      await vi.advanceTimersByTimeAsync(60);
     });
 
     expect(result.current.consoleMessages).toEqual([
@@ -114,7 +114,7 @@ describe('useConsoleMessages', () => {
     });
 
     await act(async () => {
-      await vi.advanceTimersByTimeAsync(20);
+      await vi.advanceTimersByTimeAsync(60);
     });
 
     expect(result.current.consoleMessages).toEqual([
@@ -131,7 +131,7 @@ describe('useConsoleMessages', () => {
     });
 
     await act(async () => {
-      await vi.advanceTimersByTimeAsync(20);
+      await vi.advanceTimersByTimeAsync(60);
     });
 
     expect(result.current.consoleMessages).toEqual([
@@ -148,7 +148,7 @@ describe('useConsoleMessages', () => {
     });
 
     await act(async () => {
-      await vi.advanceTimersByTimeAsync(20);
+      await vi.advanceTimersByTimeAsync(60);
     });
 
     expect(result.current.consoleMessages).toHaveLength(1);
diff --git a/packages/cli/src/ui/hooks/useConsoleMessages.ts b/packages/cli/src/ui/hooks/useConsoleMessages.ts
index 69fa7fe6e4f..8dfa4814cd3 100644
--- a/packages/cli/src/ui/hooks/useConsoleMessages.ts
+++ b/packages/cli/src/ui/hooks/useConsoleMessages.ts
@@ -9,7 +9,7 @@ import {
   useEffect,
   useReducer,
   useRef,
-  useTransition,
+  startTransition,
 } from 'react';
 import type { ConsoleMessageItem } from '../types.js';
 import {
@@ -71,10 +71,11 @@ export function useConsoleMessages(): UseConsoleMessagesReturn {
   const [consoleMessages, dispatch] = useReducer(consoleMessagesReducer, []);
   const messageQueueRef = useRef<ConsoleMessageItem[]>([]);
   const timeoutRef = useRef<NodeJS.Timeout | null>(null);
-  const [, startTransition] = useTransition();
+  const isProcessingRef = useRef(false);
 
   const processQueue = useCallback(() => {
     if (messageQueueRef.current.length > 0) {
+      isProcessingRef.current = true;
       const messagesToProcess = messageQueueRef.current;
       messageQueueRef.current = [];
       startTransition(() => {
@@ -87,15 +88,26 @@ export function useConsoleMessages(): UseConsoleMessagesReturn {
   const handleNewMessage = useCallback(
     (message: ConsoleMessageItem) => {
       messageQueueRef.current.push(message);
-      if (!timeoutRef.current) {
-        // Batch updates using a timeout. 16ms is a reasonable delay to batch
-        // rapid-fire messages without noticeable lag.
-        timeoutRef.current = setTimeout(processQueue, 16);
+      if (!isProcessingRef.current && !timeoutRef.current) {
+        // Batch updates using a timeout. 50ms is a reasonable delay to batch
+        // rapid-fire messages without noticeable lag while avoiding React update
+        // queue flooding.
+        timeoutRef.current = setTimeout(processQueue, 50);
       }
     },
     [processQueue],
   );
 
+  // Once the updated consoleMessages have been committed to the screen,
+  // we can safely process the next batch of queued messages if any exist.
+  // This completely eliminates overlapping concurrent updates to this state.
+  useEffect(() => {
+    isProcessingRef.current = false;
+    if (messageQueueRef.current.length > 0 && !timeoutRef.current) {
+      timeoutRef.current = setTimeout(processQueue, 50);
+    }
+  }, [consoleMessages, processQueue]);
+
   useEffect(() => {
     const handleConsoleLog = (payload: ConsoleLogPayload) => {
       let content = payload.content;
@@ -149,6 +161,7 @@ export function useConsoleMessages(): UseConsoleMessagesReturn {
       timeoutRef.current = null;
     }
     messageQueueRef.current = [];
+    isProcessingRef.current = true;
     startTransition(() => {
       dispatch({ type: 'CLEAR' });
     });