What is LOST.DIR?

"LOST.DIR is something mac disk repair looks for and will ask about as part of it's repair process. If it's related at all to the standard lost+found, then it's a special file that holds all the corrupted or orphaned files found during a file system check.

My guess is Wil is right, something is checking your drive and finding a problem it wants to make note of in LOST.DIR. I think this sort of thing is more likely to happen with Macs on non-HFS drives."