Windows 11 Apps on Startup change their settings

This is a surprisingly common Windows quirk, and you're definitely not alone in wanting to throw your PC out the window every time you have to manually open all your apps! Let’s break down a few causes and troubleshooting tips:

Why Do Startup App Settings Reset After a Shutdown (But Not a Restart)?​

1. Fast Startup (Hybrid Boot) is Often the Culprit
Windows “Fast Startup” combines elements of shutdown and hibernate to speed up booting. Unlike a full shutdown or restart, Fast Startup sometimes doesn’t save various settings changes (including some startup preferences). So, changes made to startup items may not persist after a full shutdown with Fast Startup enabled, even though they seem fine after a restart.
2. Sync & Cloud Account Settings
If you use a Microsoft account and have syncing turned on, sometimes Windows will "restore" app startup settings from your account cloud profile each new boot, potentially overwriting what you picked.
3. Third-Party Apps or System “Cleaners”
Occasionally, other tools like system optimizers, company management software, or even aggressive antivirus programs will revert or block certain startup entries.
4. Registry or File Permission Issues
If the method you use to enable startup (Task Manager, Settings, dragging shortcuts into the Startup folder, or editing the registry) has permission issues or conflicts, sometimes the settings don’t actually "stick" for the next cold boot.

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How to Troubleshoot (and Hopefully Fix!) This Annoyance​

A. Disable Fast Startup

1. Go to Control Panel > Power Options > Choose what the power buttons do.
2. Click “Change settings that are currently unavailable.”
3. Uncheck “Turn on fast startup.” Save changes.
4. Now set your startup apps again, shut down overnight, and see if the settings persist this time.

B. Audit Where You Set Startup Apps

• In Task Manager (Ctrl + Shift + Esc > Startup), check which apps are enabled.
• In Settings > Apps > Startup, verify what's enabled.
• For special apps, check if they have their own in-app setting for “Run at startup.”
• Check if you’re using shortcuts in: shell:startup (per-user) or shell:common startup (all users).

C. Microsoft Account Sync

• Settings > Accounts > Sync your settings.
• Try disabling “Other Windows settings” and see if this helps prevent changes from mysteriously reverting.

D. Third-Party Cleaners/Defenders

• Temporarily disable or uninstall any third-party tools that claim to “optimize” or “protect” Windows startup.

E. Windows Updates

• Rarely, some Windows updates can reset these preferences (for your "own good", of course). Make sure Windows is fully updated in case a bug has been patched.

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If All Else Fails…​

• Create a scheduled task that starts your favorite apps on logon—these tend to stick better.
• If you want a walkthrough for any of the above steps, especially Task Scheduler (it can help where basic methods fail), let me know!

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Let us know if any of these work for you or if you see any pattern with particular apps. Windows can get stubborn, but so can we!