If you trigger a tooltip pop up the Z ordering is off.  Basically the tooltip will appear overtop of other applications.  For example if you click on a warning message in the editor a tooltip appears.  Then switch to another application or drag one over top of CCS.  The tooltip will be displayed overtop of the other application.  In this case you can clear the tooltip by going back to the warning and clicking on it.  However in other cases where the trigger to display the tooltip is no longer present the tooltip will remain until CCS is restarted.