Where is the Visual Studio layout saved?

• Export your current settings. Don't choose to export the layout settings.
• Reset IDE settings to your favorite
• Import your exported settings

You might want to try Window > Reset Window Layout. This will reset the windows the way they were configured the last time you imported a layout.

Some of the layout information is stored in the registry for the current user.

HKCU:\Software\Microsoft\VisualStudio\9.0

If you're really having a lot of problems you can take the desparate step of deleting or renaming this key. Personally, I would rename it, start VS and see if that fixed my import export settings problem.