Maybe it's rather a problem of the old Hatari version (0.95) available for Maemo, than a specific problem of the Maemo port. With older Hatari versions even on my desktop PC sometimes I did encounter strange mouse behaviour. With the most recent version 1.2.0 I don't have such issues. Unfortunately I have absolutely no experience with porting stuff to Maemo. :-( And as there was a major code cleanup in Hatari 1.0.0, applying any Maemo specific patches from the 0.95 port ot a more recent version might not be that straightforward...