If you deleted your files/folders to the recycler and then emptied that, the files will be renamed in XP and Vista.
Apart from that just running stuff on your pc can overwrite file entries in the MFT very quickly (a simple prefetch file, for instance), but I wouldn't expect that to happen to all files.
I would sort the Recuva output by size or date last modified order, in an attempt to locate them. Recover any suspects to a flash drive before looking at them.