@Lordmonkus: Ya I tried that too, in the end I don't have an issue with having cart based games organised differently. When it comes down to it I think I really need to re-organize my cart Nintendo and Sega stuff better. I am starting from "scratch" with organization after losing my old hard drive. Having complete no-intros for cart systems is amazing, but at the same time sucks trying to organize.
@DOS76: MAME is the last thing I was going to import as I know that it "can" cause import problems. I also don't have the the harddrive with those on my person at this time. A friends is setting up a cabinet and is barrowing my HDD because he is no longer able to DL them himself.
Everything seems to be working now. I made sure to double check that there was no hidden system under manage platforms, and Double checked the .XML files for systems that I am having difficulties with. I will re-up is any more issues arise.
Thanks All,
-Arctic