I thought that you couldn't LAUNCH the game...not that you couldn't SEE it in your list!!
I would have directed you to the "show available roms" option directly!
mGalaxy's "Show available roms" is ONLY looking into the "roms" folder residing at the same level than mGalaxy!
So, it won't check into a renamed "roms" folder or a folder moved somewhere else!
As you know, mgalaxy has been written to be as "simple" as possible (and it is loved for this same reason ;-)...so, unfortunately there's no "complicated" configuration menu!
But I understand that the functionality that you're looking for may seem a very basic requirement to you!?
So, if many user might want it, I could add this option (and others) in "mGalaxy Runway".
mGalaxy Runway could become a "mGalaxy's Preference" application and manage keyboard mapping and other options like the one you need now.