Does reverting 800x480 to 640x480 in config solve more problems than it creates for most users with regards to de-sync at borders? I know 800x480 isn't a standard resolution for DOS games (if at all supported), so was this only purely a change made for supporting windows. If reverting this reduces the de-sync of mouse in the majority of cases, I'll try pushing a build with the defaults set to 640x480
I still would like to be able to solve the initial offset fault as some stage, when I can find time.