Depends on what's actually happening. Sounds kind of cool actually, but probably not when you are trying to do something productive
You can try restarting just the X server and see if that brings it back. Next time it 'disappears' type:
CTRL + ALT + BACKSPACE
And it should kill (and probably restart) your X server. Log back in, and see if you have your mouse back.
If not, it may be a gpm issue. Depending on your distro, it may have gpm as an init script, in which case:
May fix your problem.
There's a few ideas, good luck!