To eliminate the game you don't have, go to the "preference panel" (when you are on magalaxy) on top there is a filter option " show available" (Sorry not sure for traduction). With that you can use a complete database.
And this checkbox need to be checked for mgalaxy can use database to convert file name in rom name.
I can't undertand, why it don't work, but yes, you can try to remake the database, and use the filter to don't display the rom you don't have.