The problem with animated mouse cursors disappearing (like the loading cursor in Firefox) is described
here [beryl-project.org]. Apparently the 'Scale the mouse pointer' and 'Hide original mouse pointer' options of the Enhanced Zoom plugin from Compz Fusion work by changing the size of the cursor to 1x1. After zooming out the static cursors are restored, but the animated are not. This is also why the bug appears so random. It only occurs after the first usage of the zoom function.
The solution is to disable the options mentioned above, and probably use the 'Sync Mouse' option, log out and log back in. The size of the cursor will now always stay the same, but it will also not disappear anymore.