Ok, I've been able to reproduce one pointer slow-down 100% of the time.

If I'm typing in a text box in programs within my VMWare Windows XP and the mouse cursor blanks (because I'm typing), moving it again causes it to appear and move very slowly for the first bit.

I thought this might be the universal cause, but it doesn't seem to happen in this text field in Safari. I'll keep my eyes open for more specific cases.