This problem is caused by a bug in Windows that causes the taskbar tool-tips to lose their "topmost" window style and be covered up by the taskbar. Microsoft has acknowledged this problem exists (http://support.microsoft.com/kb/912650), but has not yet fixed it.
Check out this web site for more information and a permanent fix:
Tool Tip Manager was written specifically to fix this annoying problem by processing taskbar window messages and resetting the "topmost" window style for tool-tips as needed, automatically. This program also allows you to customize the appearance of the task bar tool tips (font & color) and set the automatic hide timer value.