Mystery solved. I put the hotkey lines in my main retroarch.cfg and it worked like a charm. I now have a SNES pad and wired xbox 360 setup on auto.
The Select and Start buttons on the SNES correspond to the XBOX 2nd L & R triggers which none of the emulators use, so it works out well.
Only issue is that retroarch freezes when I swap controllers. Not a big deal b/c who the heck swaps controllers mid game anyways. :-) I think the autoconfig still has some bugs to work out.
Thanks for helping me troubleshoot.