Fixed my problem. Figured I'd post the resolution in the event that somebody else inevitably has the same issue. gunnarh's posted solution was right. It's not an issue of the multiple joysticks. It's actually the sketch. You need to use the bounce library, like was used in gunnarh's link. Without it, the buttons don't get recognized properly within retropie. I went as far as to edit the usb_desc.h for the teensyduino libary to only have it expose the joystick, and nothing more. That worked for only having a single joystick show up, but the button issue remained. It wasn't until I utilized the Bounce library, that my button presses behaved as I expected.
