There's a chance it may be doing a chkdsk on every boot now. Search on "clearing the dirty bit" or something similar. When you try to do a chkdsk C: /f say, the file system can't be fixed while it's running Windows, so it sets the "dirty bit" meaning on next boot do a chkdsk /f for the drive. You cannot clear the dirty bit with a file system command.

chkdsk has to run and clear it. There's an article out there somewhere that tells how to deal with it. So search on "clear dirty bit" or "chkdsk runs on every boot" and you should find it. Probably MS KB article but likely there's other articles on tips sites(maybe including this site.) Sounds like that's what's happening.