I'd be nervous too. Did you select the verify option for your backup? I'm only familiar with FMS 10 so if you are using an earlier release, I don't know if you have this option or not.
Lot's of flaky things can happen if a file's indexes aren't in perfect condition. The recover process is one way to rebuild a file's indexes from scratch--though I never recommend using the recovered unless there is no other option.
Yeah, verify is on. Thanks for the thought.