I'm running Ubuntu 13.04 64-bit, after I installed ubuntu I installed quite a number of packages (Several Gigabytes worth), when I restarted I found that the mouse cursor was invisible, when I opened up firefox I could see it normally but as soon as I moved it off firefox it vanished. I tried several other programs but it acts the same.
Finally I went to the extreme and deleted all . folders and moved most all of the . files to a Backup folder except for .bashrc .profile and the like but it's having the same problems.