Hey rbaker, thanks for the response. I ended up reflashing the sd with a new image of retropie. Previously i had retropie installed manually on top of raspbian. This is fine because i really dont use the pi for anything but gaming. I'm sure one of the scenarios you mentioned was the problem. It seems like probably the folder structure was corrupted at some point and no longer being correctly picked up by retropie.. i guess =)
Reflashing with the newest version of retropie worked like a charm, all my original roms work. Now im on to trying to get metal slug 5 to work correctly! xD
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