Sounds like the issue I just had. I took my ext USB drive (WD IDE in a Vantec case) with 200GB of music to a friend who had just acquired that day a new Vista machine. It mounted just fine but... no folders. I checked on drive properties and the space was being used, so the files were still there. But even odder is that running a search on that drive found the files! Yet, no folders in either Windows Explorer (or whatever Vista calls it) or any other app.
Nonetheless, when I plugging it back into my XP machine every thing was there (thank God!)

If any one has an explanation for this I'd be gratified to hear it.