Try closing and reopening ArcCatalog.
I have been annoyed with ArcCatalog caching the layers that exist when I first connect but does not refresh them until after I close and re-open. Even the refresh command does not update the cache, just reloads the display from current cache.
Can you zip the file geodatabase and post it (or send it to firstname.lastname@example.org). I'll take a look and find out what the problem is.
What version of ArcGIS are you using?
Can you send my your contact information (full name, company). I'm having a FTP site set up for this.