I read something just the other day about a bug. If you add a resource, then you delete it, it makes for trouble in the backup process. I tried to find it to give you link to the posts and within the posts was alink to the bug tracker on it. Maybe others that can remember where that post was can chime in here? It was within the last 2 or 3 days in the Using Moodle postings. I will keep looking, but I figure if you knew there was something out there you could be scanning back for it as well.
(sorry about the odd font issue in the post. I am not sure what happened and the editor refuses to make it all the same for me)