Apps and windows toggle on and off and are unusable without clicking back into same.

There is an OS-level "Phantom Focus" bug is a known issue affecting recent macOS updates (including macOS 27 Golden Gate). It causes the active window to suddenly lose its responder chain, acting as though a hidden background process or system alert has momentarily hijacked your keyboard input.

Even if you have already uninstalled or closed your main third-party apps, hidden system services or lingering background helpers are likely still triggering the issue. You can try the following steps to track down and cure the issue:

Clear Your Background Login Items

Many users have isolated the issue to legacy update agents or background daemons running invisibly in the background.

• Open System Settings and navigate to General > Login Items & Extensions.
• Look under both Open at Login and Allow in the Background.
• Toggle off everything that is non-essential (even utilities you think are inactive).
• Restart your Mac to see if the focus drops stop.

See also: Manage login items and background tasks on Mac - Apple Support

Note: If you use the network monitor Little Snitch or certain third-party VPNs, they are heavily documented to cause immediate focus loops. 

Identify the Culprit via Terminal

If the drops keep happening, you can run a simple terminal command to print the exact name of whatever process is taking over your screen the millisecond it happens.

• Open the Terminal app.
• Paste the following command and hit return

python3 -c "import Cocoa; import time; last_app = None; print('Monitoring focus changes... Press Ctrl+C to stop.'); print('-'*40); while True: active_app = Cocoa.NSWorkspace.sharedWorkspace().frontmostApplication(); app_name = active_app.localizedName() if active_app else 'None'; (print(f'[{time.strftime(\"%H:%M:%S\")}] Focused app: {app_name}') or (last_app := app_name)) if app_name != last_app else None; time.sleep(0.1)"

• Keep the terminal window visible and continue using your computer as normal.
• The exact moment your app loses focus, look at the terminal. The very last item printed will reveal the name of the rogue system daemon or hidden app causing it

If you have 3rd party ‘protection’ software installed, that may be the problem. That includes:

• Cleaners (software claiming to automatically free up space)
• Optimizers (software claiming to make your Mac run faster)
• Antivirus software
• VPN software (unless provided by a school/employer to enable access to internal resources from a remote location)

Such 3rd party system ‘helpers’, ‘cleaners’ and ‘protectors’ do more harm than good. In fact, such products are completely unnecessary for macOS and the only ‘good’ (if you want to call it that) they do is to put money in the developers’ pockets. Cleaners and protectors cause compatibility issues, often after macOS updates. Commercial VPNs claim to hide your browsing activity from websites, and while that may be true those VPN providers just sell your browsing data to others. For the user, all of these types of software offer only harm…and if that is limited to harm to your bank account, then count yourself lucky. If you have installed such software, follow the developer’s instructions to completely uninstall it (note that some developers fail to provide instructions and their software installs can be pervasive, meaning the only way to truly remove it is to erase your Mac, reinstall macOS then restore your user files from a backup).

It might help to download and run EtreCheck, written by a long-time forum member. The free version is fine. Post the full report using the Additional Text button. No personal information is revealed. 

Systematic Troubleshooting Statement: Repeated Application Focus Loss in macOS Golden Gate 27.0.1

1. Problem

After upgrading to macOS Golden Gate 27.0.1, my 16-inch Apple silicon MacBook Pro loses focus from the active application every 3–5 seconds. Safari and other apps remain visible, but the window’s traffic-light controls turn grey and keyboard/mouse interaction stops until I click the window again. It also occurs while idle and affects multiple apps.

Restarting, disabling startup items, testing without peripherals, and reloading macOS have not resolved it. The cause is unconfirmed; possibilities include an OS window-management/input regression, background software, account configuration, or hardware.

2. Diagnostic Procedure

Step 1 — Check version and updates

Open Apple menu > System Settings > General > Software Update. Record the version/build, check for updates, and back up before updating.

Apple: Update macOS on Mac - Apple Support (CA)

Release notes: What's new in the updates for macOS 27 Golden Gate - Apple Support (IE)

Step 2 — Monitor background processes

Open Applications > Utilities > Activity Monitor and reproduce the issue. Search for MenuBarAgent and note whether it becomes unresponsive when focus is lost. Record timestamps and errors. Review System Settings >> General > Login Items & Extensions. Quit non-essential third-party utilities one at a time, especially window managers, keyboard/mouse tools, clipboard managers, screen recorders, and menu-bar apps. Do not indiscriminately disable Apple services or repeatedly force-quit system processes.

Apple: Change Login Items & Extensions settings on Mac – Apple Support (UK)

A MenuBarAgent correlation is a lead, not proof of cause.

Step 3 — Check input/window settings

Review Keyboard > Text Input and Keyboard Shortcuts > Input Sources; Accessibility features affecting keyboard/pointer behaviour; Stage Manager (temporarily turn it off if enabled); and Displays > “Displays have separate Spaces” (record the setting first). Change one setting at a time.

Step 4 — Test Safe Mode

Shut down. Hold the power button until startup options appear; select the startup disk, hold Shift, and choose Continue in Safe Mode. Test Safari and another app for 5–10 minutes, including while idle.

• If the issue disappears, software active during normal startup becomes a stronger suspect.
• If it persists, a system-wide cause remains possible.

Apple: Start up your Mac in safe mode – Apple Support (UK)

Step 5 — Test a new user

Go to System Settings > Users & Groups and create a temporary standard account. Log in without importing settings or installing software, then test multiple apps.

• If the issue disappears, investigate the original account’s preferences, background agents, extensions, and login configuration.
• If it persists, a system-wide issue becomes more likely.

Apple: Change Users & Groups settings on Mac - Apple Support (IE)

Step 6 — Run Apple Diagnostics

If the issue persists in Safe Mode and a new account, shut down, disconnect unnecessary accessories, and hold the power button until startup options appear. Release it and press Command-D. Follow the instructions and record reference codes. A clean result does not rule out software.

Apple: Use Apple Diagnostics to test your Mac – Apple Support (UK)

Step 7 — Escalate

If unresolved, contact Apple Support or submit macOS feedback. Provide version/build, Mac model, onset after upgrade, frequency, affected apps, whether it occurs while idle, MenuBarAgent observations, Safe Mode/new-account results, diagnostic codes, and relevant logs.

Feedback: Feedback - macOS - Apple

Apple Support : Contact - Official Apple Support (CA)

Suggested report:

“Since upgrading to macOS Golden Gate 27.0.1, my 16-inch Apple silicon MacBook Pro loses application focus every 3–5 seconds. Multiple windows remain visible, but their traffic-light controls turn grey and keyboard/mouse interaction resumes only after clicking the window. It also occurs while idle. Restarting, disabling startup items, testing without peripherals, and reloading macOS have not fixed it. Please investigate a possible system-wide window-focus, window-management, or input-handling regression. I am checking whether MenuBarAgent becomes unresponsive and can provide Safe Mode, new-account, and Apple Diagnostics results.”

3. Regression Assessment

Community reports may be useful leads but do not confirm an officially recognized macOS bug. Treat a regression as a hypothesis until supported by evidence or Apple confirmation.

Immediate priority: Record what happens during focus loss, especially MenuBarAgent’s status, then perform Safe Mode and new-account tests. Back up data before major changes; do not erase the Mac or reinstall macOS again without a clear reason and Apple Support guidance.

After updating to 27.2 the problem came roaring back and did not go away. Subsequent testing revealed that the Micromat Inc app (Techtool Pro), when disabled, stopped the annoying behavior. Of course it had to be updated, have done so, and everything is working correctly. Thanks again.

Thanks for this. After letting it sit overnight, it appears to have stopped. Good thing I wasn't depending on the Mac for getting any work done yesterday. Am bookmarking this in case it reappears. Thanks to both for the insights.