It sounds as though the collection may not be fully downloading properly. Try enabling -condebug via the server control tab in your control panel and viewing your console.log file in FTP, it should list information about the collections and if they downloaded properly.
You may also want to try another small collection as a test to see if it's working properly.
@Kraze^NFo> Juski has a very valid point
@Juski> Got my new signature, thanks!
@Kraze^NFo> Out of context!
@Juski> Doesn't matter!
@Juski> You said I had a valid point! You can't take it back now! It's out there!