Yeah, that brings back happy memories of losing all my work and having to restore everything from floppies!
The cabling / drive issue is well worth checking out. If you're using a straight 40 - 44 Pin ribbon cable then you might want to replace it as they're not that robust in my experience. If you've got a bufferred interface then there may be an issue there.
Other things to consider are whether the drive is being fully formatted or quick formatted. The former takes time but sorts out a lot of problems. Max Transfer settings in the HDToolbox menu make a difference too.
