This is being tracked here: Configuration window appears out of the blue
Hope to find a solution, but so far I have no clue ;-(
The only thing I have noticed so far from the logs I received, they all seem to be coming from some pretty advanced users. Not sure yet what they have in common.
Closing here to avoid confusion!
Ah and you could use the predefined action „Show BetterTouchTool preferences“ if you have used the terminal command to workaround the issue