OK, by reading the message from Dan I get the idea of what's your problem:
you've selected "show available roms only"...but you have selected "show clone:off" too!!...so mGalaxy only show you the roms that you have AND which are not clone of other roms
You'll see that if you select "show clone: on" you'll get the full list displayed.
Replacing the "cloneof" by "clone" in the "mg_mamedb.xml" file would simply skip that clone rom functionality and make it unavailable.
Please tell if your problem is solved with this advice, thanks