I just ran across this today. Trial and error finally yielded a bingo. I had too many files in the root directory of the ScanSnap docs. I created a Mscl folder within my ScanSnap docs tree, then dragged + dropped most files there. This eliminated the disk-full error message, and ScanSnap returned to normal.
how big is the drive that holds your "My Documents" folder? if you are scanning multiple, colour, double-sided pages at high quality resolution you may end up with a single doc that will take 100MB+...
Yeah, I've been using a couple of ScanSnaps for over a year, with no problems til today. Like you, I have a 500g drive, so I was stumped. When rebooting brought no relief, I literally sat and stared at my file mgr, trying to figure out what, if anything, changed. That's when I realized that I'd been lazy/ sloppy the past few weeks- not bothering to organize the docs into assorted folders. Live & learn, eh?!
He means MISC, for Miscellaneous. Just create a new sub-directory, then drag n drop your files in there. The root directories apparently fault when they get too big, so you have to reorganize every so often to keep the roots clean.