So I managed to solve this, but I'm not entirely sure how. I fixed the under-voltage issue with a better power supply. Entered a game and had the same issue. Remapped after exit, then decided to see if it would do it again with other emulators, and like magic, I could never get the issue to reproduce even after a reboot. So.... I have no idea. My guess is it was related to the undervoltage and the board wasn't getting enough power causing a small memory dump when exiting the emulator.

The PS4 DS controllers show as 2 devices - one for the touchpad and one for the actual gamepad, that's why you have 6 listed. There are some hints on how to disable this in this topic.
Also, please add the info detailed in https://retropie.org.uk/forum/topic/3/read-this-first when opening a support topic, it's easier to diagnose things.

@fallen86 I'm in the middle of a rebuild or I would send you my config to help. I learned my lessons about backup the hard way. It's been a while and I did use joystick selection tool, but I rarely played 2 player games the way you are. My biggest concern was mapping a specific USB controller to each game.
I have a feeling the problem is with the driver for you, because the tansktick functions as a keyboard and the driver is working around that to emulate a USB gamepad. Good news is if that doesn't help solve the problem, it's easy to roll back to the driver.

Did you get it working? I've been trying to do the same thing, but can't seem to make it work. Right now player1_start begins Ms. PacMan for 1 player and player2_start begins Galaga for 2 players. I've tried going into the FBA menu to change the controls but when I cycle through the buttons, the only available start button is "Start (left)", which both player1_start and player2_start are bound to. Any help would be awesome!

@jlvandusen what do you mean it was ignored? Are you certain you have the right index number?

I did try the Xarcade2Jstick driver, but wasn't happy with the results.
I did not follow the instructions at https://github.com/RetroPie/RetroPie-Setup/wiki/X-Arcade, but rather chose the driver from within RetroPie, if I remember correctly. I know I never did a sudo make or sudo make install.
Although the other method I followed was much more time consuming, I'm very happy with the results.
My retroarch.cfg never had any commented lines to begin with, so I'm not sure why it was different than what I found on GitHub. I used the 4.2 SD card image directly from RetroPie.

@jeremyxgaming Clean install of what version? Mine stopped working in lr-MAME2003 recently and Im trying to figure out why. I did a clean 4.3 install and its still not working :(