i've had a similar problem. i've got Panther running on a 15" PB (new 😀) and i was just using Painter 8 and Photoshop today. whenever i went to change colors in Painter the cursor would disappear, then come back a few seconds later. i've got MenuMeters installed, and i noticed that whenever the cursor disappeared CPU load was at 100%, and i was working on a fairly big document in Painter.
my guess is that it might disappear sometimes under a high CPU load. but i've only experienced it in Painter. i don't think it's anything to really worry about (at least in my case) but it sure is annoying.