Account data getting lost

[Arran]

Well we had to stop our server today for windows updates. We kicked all the players (to save their data) and shutdown the server with command. But on return some of the accounts have not saved correctly, one person with 64 hours play time became 47 minutes and everything they had done in those 63 hours were lost.

This has happened once before when stopping the server, the accounts do not seem to be saved properly. We did hourly backups since then but the database file doesn't seem to be saving right. Has any other servers had a problem like this before?