Ccleaner has an option to over-write files set to be deleted, several times if necessary.
Perhaps a possibility exists to recover files erased in this manner, using specialist forensic gear, but nobody seems to know for sure. I tend to think that recovery of such files might be in the "urban myth" basket. Still, who knows what's possible?
@lasernigel, it sounds like a malicious process running. Try
MBAM. Download it, install it, update it, set it for a quick scan, remove anything found.