I have my steam library pointed to a separate drive (A:\) with my downloads folder being in the default location. I have both FO3 GOTY and NV installed to my A:\ drive exactly as they were when steam downloaded them. .
The installer failed to automatically find the install locations (which is fine) but when pointed to the correct locations manually, it would fail to find any of the files in those directories when running the installer from the default C\users\user\download. Moving the installer to my A:\ drive lets the installer run just fine.
Obviously this isn't a big issue since I got it to work just by moving it, but I don't think this is intended behavior and the bug tracker didn't seem to be the place for installer bugs.
(I can provide additional system details if needed)