I had this really early on with my cube, with 10.0.4 and then never had it again until 10.2 on my new dual867. I have to log out and back in to restore the cursor. Button and menus will react to where the cursor should be showing.
I never had this problem on my two cubes since installing Jag and it has happened only twice since Aug 24 on the dualie. It was always after waking from sleep and Classic was always running.