Well, now that the simple stuff is out of the way, then it's probable that the directory tree got "pooched" somehow.
I checked ATP's site to see if they offered any file recovery tool but found nothing(my SanDisk Extreme came with a file recovery tool on CD).
There are several programs that can help you recover your images, and you can purchase them and download them on the spot. There is one that allows you do full recovery with the evaluation version:
Digital photo recovery - ZAR image recovery function - Not recommending it as I have never used it, just telling you it exists and could possibly work for you.