Have you tried it with a different mechanical HDD? I’ve had hard drives fail right after chkdsk /F /V /R /X reported that there are no errors or bad sectors.
Found my problem… loaded up my original 14.04 ubuntu… and found that some of my tables in the fog database were corrupt. I ran the repair on them and that fixed it 🙂
mysql -u root -p fog
mysql> REPAIR TABLE userTracking; -----> this is an example of one table messed up