Hm, I don't know what could be causing that. Have you tried changing to fullscreen or fullscreen windowed mode, or turning mouse capture on or off? (edit init.txt to change these things; there are instructions in the file).
Could you try changing to fullscreen or fullscreen windowed mode, or turning mouse capture on or off? The init.txt file has options to do that. I'd be interested to know if that works (I haven't been able to reproduce this problem on my own system).
