I've had a problem in which the mouse cursor sometimes disappears from the screen and takes a few seconds to come back. I had it happen in safari a few times, and now I had it happen when I just started up the computer. This isn't the normal mouse disappears when you type thing and comes right back when the mouse moves because I wasn't typing anything when starting up the computer, and in safari I moved the mouse and the pointer didn't immediately appear, it took around 5 seconds of moving around the mouse for it to come back. I just repaired permissions today, so that isn't it, because it happened again after that.