Steve,
FileSalvage would probably do the trick. You can DL the trial mode and see if your lost files are identified/located. Alas, that's about all the demo mode is good for. If you want to recover the files, you must first obtain a registration number ($9.95 US).
Also, a few guesses-
I. Try your flash drive on a different machine (even a PC).
II. After inserting your flash drive and opening it, Select All (Command+A) and then drag the contents to your desktop. Maybe the lost files will then appear.
III. Use a utility such as FileBuddy to do the search. Sometimes a third party search will find things the Finder doesn't.
Good luck and please let us know how this saga ends.
Sorry my help is not much. But perhaps others, with better suggestions, will stop by.