Since today I have a timer overlay at the top left, which I can't move or disable (didn't found anything within the settngs).

It is not by design. Does this come back when you restart the app?
Yes, this is permanent, even after a restart. I also have this issue on two different PC's.
I noticed that logging out from the app and logging in again "solved" this (at least on one the devices).
It also disappears after a couple of minutes on its own.
This looks like the hover-tooltip of the notification icon on the taskbar.
@scrobbleme:
If the little box visible, does anything happen if you hover on the Toggl Desktop icon (in the notification area / systray) for a few seconds?
@amulware No, nothing. The box doesn't seem to be there for the mouse. When I hover or click the event is propaged to the app behind the box.
So far I have not been able to reproduce this. It seems like it only happens under specific circumstances.
Closing this until we get more information that helps us reproduce it.
The bug is still present, though not sure how to reproduce it
I encountered this bug randomly after using Toggl Desktop for a few months. I found this thread. Clicking on the Toggl logo in the sys tray fixed it for me. Windows 10.
thanks, @linnflux. It suddenly showed up for me this morning after using Toggl Desktop for a couple years. Your method fixed it for me, too. Also on Windows 10.
Thanks @linnflux. I can also confirm your fix works for my version of the latest version of Toggle(to date) on my Windows 10 computer as well
Most helpful comment
I encountered this bug randomly after using Toggl Desktop for a few months. I found this thread. Clicking on the Toggl logo in the sys tray fixed it for me. Windows 10.