@mitu This was it! I have a script that controls an LED light/Power button on my case, (as well as shows heat/fan speed, etc) and it seems that the new update doesn't like it. If I delete the python line, the retropie command line and the RetroPie UI work as expected. Not sure what the conflict is, but it's clearly to do with the script on my end.
Below is the autostart.sh if you're curios. Thanks so much for your help!