I get a lot of problems with the mouse using gnome. A simple and easy to reproduce problem is to click anywhere on the tool bar across the bottom. The result will be none of the mouse buttons will then be recognized. Other problems I see are the mouse cursor disappearing completely. In both of the above cases I also end up unable to change the focus -- whatever window that last had the focus keeps it. In all cases the only way to recover is to bring down X and restart. I don't have this problem if I switch to AnotherLevel, so it looks like it's something gnome related (or enligthenment maybe) and not X-server related.