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, but has not yet fixed it (it's been around for at least 3 years).
Check out this web site for more information and a 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.