Welp, I erased the original TQ EPROMs and reprogrammed them and it did not solve the problem. So I am stumped. This is very discouraging.
I did take a bunch of pictures of my TQ board so that I don't have to take the top board off to see what's on the bottom board again (it is a huge pain to get it back together).
This means that my fix for Thayer's Quest on Dexter is delayed indefinitely. :(