Are you running the Aero Glass desktop?
This is not FO3 specific advice but it does concern windows/menus issues:
[Edit: Geez, I could have been a wee bit more specific...
These options are accessed by right clicking on the FO3.exe > Compatibility tab. That should show you these options mentioned below.]
2. Check the option to disable visual themes. This will disable theme support in the application, and is a good choice if you're noticing problems with menus or buttons not being drawn correctly.
3. Check the option to disable desktop composition. This will disable the advanced features in the Aero Glass interface, such as transparency. This is a good choice if you notice problems with windows not being drawn correctly. For example, if the IDE includes visual tools to create and edit forms or dialogs, you may find that controls are drawn very slowly or aren't redrawn in the correct position. Disabling this feature will often correct the problem, however it will force the entire desktop (not just the application) to disable the Aero UI until the program terminates.
Source: http://www.catalyst.com/products/sockettools/windows7.html
It also mentions trying to run a problematic program/app in compatibility mode for Vista w/SP1+ or XP w/SP2+. Something to consider.