well....try CHKDSK d: /F /V
which will prolly make you restart and have it run automatically, but i believe thats what i used to help me find laaarge groups of files that spontaneously disappear...

although by the same token, i think that program has also been responsible for cleaning file indexes (aka. deleting random folders), and ive never figured out how to solve THAT problem

i think chkdsk can also be activated through the drive properties > tools > error-checking button