I had a bit of a strange problem with the library in VMC it started to display folders that I had not added for example the root of c: and my music was being displayed in the videos section, I tried to remove all folders from within media centre and also from within media player but random folders still started to appear.
So I thought their might be a problem with the database but their is no obvious way with media player to repair or delete it, this needs to be done manually.
Clear all watched folders from WMP 11
Clear all libraries in VMC
Delete all files from c:\Users\[username]\AppData\Local\Microsoft\Media Player (where the database is located)
Re-Set up libraries in VMC