Have you just upgraded from Access 97 to Access 2000? Have your autonumbers reset in your tables? The problem is that Access 2000 requires a patch in-order for it to compact a database without destroying it! The database gets compacted automatically when you convert the database from 97 to 2000 versions.
The other problem is that the database you have compacted is corrupt and isn't fixed with the patch. I haven't come up with a solution for this. I went back to an old version and then compacted with the patch in place.