I can get to the core options using select&start anyway. (Those two are the only buttons that function) I couldn't find the option at first (because one would think that would be in the Controls menu...) but I found it and it now lets the joysticks work, at least. I have to check the buttons on a different game (because pacman has no buttons). I'll set it at the Core level once I test it out. So far, so good.
EDIT: I think it's working properly at this point. Thanks!
I removed the #emulationstation #auto line 2 of the autostart.sh, and it worked. I didn't think that line would matter since it doesn't effect mame2003 roms launched the same way. Why does multi lines cause this issue? Is there a way to include multiple lines?