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OK, I've checked the issue.

The tweaker shows the "Could not open explorer's process" error because it can't inject to an elevated explorer process, and this cannot be fixed.
The tweaker has to be run as administrator too to be able to inject successfully.

As for the tray icons - it has nothing to do with the tweaker's error message. The reason is that applications can't send a notification to the elevated explorer to create their icon.
I couldn't make the option work for explorer, it seems to always run as non-administrator.
Are you running the tweaker as administrator, too? Do you see any error message?

The issue of the tweaker silently failing to inject should be fixed in v4.2.3.

There's a bug in Windows which may cause unresponsive windows to move to the right end of the taskbar/group. Maybe this is the cause for the behavior you're seeing.

I do not think it's a bug of the tweaker. You might want to try running with it turned off, and see if the issue still occurs.