Thanks. After a bit of tinkering I did find that the retroarch.cfg was the issue. Is there software I can use to figure out what my button mappings should be?
EDIT:
Got it! Posting in case anyone finds this while searching. Check this extremely useful post:
xbox controller config
That will allow you to go through and map everything button by button, and it will append the correct mappings to the bottom of your retroarch.cfg file.
Once you have that, include the following two lines in your cfg so you are able to exit your emulators. Obviously use whatever button mappings that you need based on what was appended to your config file.
input_enable_hotkey_btn = "8"
input_exit_emulator_btn = "9"
It would be really nice if the devs would automate this process into the same process used to map the buttons for EmulationStation .. but for now I guess we have to do it manually.