Hello,
Sorry to hear you are having issues. Not sure why it happen on your system. But, instead of rebooting, have you just try restart explorer.exe and see if the issue resolve itself? https://www.howtogeek.com/198815/use-this-secret-trick-to-close-and-restart-explorerexe-in-windows/

Thanks
Basj,
Stardock Community Assistant.

Are you using the enhanced taskbar and small size? Are you using ExplorerPatcher and if so, is it up to date?

I’ve seen this issue reported before, but I can’t remember if there was a solution. I have searched the forum, but I was unable to find a reference with ver. 2. There were several with ver. 1.

Maybe Neil can shed some light on this issue.

May I know which version of Windows 11 you're currently on?

Thank you,

Basj,
Stardock Community Assistant

Please try this, uninstall Start11, reboot immediately after uninstall finished. re-download Start11 latest version from your product account page: https://store.stardock.com/myaccount/products. Install it, reboot again immediately after install finish. Retest it and report back.

Thank you,

Basj,
Stardock Community Assistant

Here is a post that discusses the same issue with Start11v1 with touch capabilities. Not sure if it relates to your issue.

https://forums.stardock.com/522807/weird-start11-taskbar-icon-alignment-issues

From this post:

"When you boot the computer from scratch, It takes a moment to initialize the touchscreen, so for a while, as far as the OS is concerned, there is no touchscreen present. So when Start11 starts, in this period, it assumes there is no touchscreen present.

"When you have "Taskbar Touch Screen Detection" set to "automatic", Start11 ends up in setting "not touch mode device". If you set to "Force Touch Mode Device" On computers that have touchscreens, the mis-alignment problem goes away."