I have this issue and from what I discovered a lot other people do - my pointer disappears. I can see stuff beneath reacting to the movement, but the pointer is gone. It happens rarely, but is confusing enough. Cmd + Tab to Finder fixes the issue, but then when going back to the browser, the pointer is gone again.
It mostly happens in Safari and Chrome. I haven't seen any solution that works.
I'm using OS X 10.8, but this problem existed before that too.