@quicksilver I have 6 button setup working on both emulators as of now. I found the settings you mentioned in Mortal Kombat II but changing them made no difference. I went over everything on my setup and was stumped. I booted up a fresh image, completely up to date, configured my SNES and Xbox controllers and put on my Sega games only. I made the changes to the respective config files and presto it works. After changing the setting you pointed out that I missed earlier in Mortal Kombat. I don't know why my original setup was not working. It has to be something I modified but I haven't found it. Thanks for you help and if I track it down I'll let you know.
Update: I think I found the problem. When I updated in the morning I did both binary and source, I've never used source before. It wrecked my controller configurations. It had my generic SNES listed as generic and just SNES, and the Xbox controllers were listed as generic Xbox, the original config, and Xbox 360 Pro. Every game I launched listed the two controllers I had connected twice and then worked in piece. Not sure why updating from source would do this as I have updated from binary and it was fine. In the future I will probably unplug all controllers and use the keyboard for updating.