I'm having similar problems. The issue typically occurs when using a custom start logo and having "enhance the taskbar" enabled. I usually restart my pc and it goes away for some time. I usually notice the problem returning after waking up from hibernation or sometimes after exiting fullscreen games. I've followed the steps above, and I've reinstalled windows twice and noticed the same problem on my other computer.

EDIT: I've noticed the problem happening more on my dual-monitor setup. Only the main monitor has the double-start menu issue, whereas the second monitor has never experienced it.  On a single monitor, the issue usually occurs after every other wakeup from hibernation. 

These are my settings:

I've tried that a few times. I've done it on fresh installs of windows 11 at least 3 times, and the problem eventually happens. 

An easy way for me to replicate the problem was to have a dual-monitor setup and to mess around and activate/deactivate the following settings a few times:

- "Let Start11 enhance the taskbar."
- Use a custom start button image
-restart explorer

After a few times, my taskbar buttons are no longer combined. It will sometimes reactivate the custom start button when it was previously disabled after restarting the explorer. But I will see a double start menu after 2-3 toggles.  Typically, when this problem arises and a reboot does not resolve it, I deactivate the enhanced taskbar, restart the explorer, restart the PC, reactivate the enhanced taskbar, and reboot again; this procedure usually resolves the issue of the double start menu for some time. It's just frustrating that this problem has been happening for a few months now. 

As for my single monitor setup, the problem is rare, but restating the PC usually resolves the issue for me