Anyone have any clue what's going on here? I have already swapped out the two 40H368's. Super Mario USA is one of the only games that seems to be working still funny enough. Wish I had a 'scope. 
I'm having a lot of difficulty thinking of a reason that it would work in some games and not others... subtle timing flaws? Stray capacitance?
Utterly bizzare... I was poking around with a high-ohm resistor tied to +5V and touched pin 39 on the CPU. It made it snap out of it. Now all games work again..? (without said resistor) What?
Super Mario USA is known to use a different controller reading routine than most other games, since external controllers doesn't work for it. Maybe that has something to do with it working.
39 is the strobe.
If a game that doesn't read controllers connected to the DA15 expansion port (bit 1 of $4016 and $4017 read) works, but a game that does read those controllers doesn't work, one possibility is that games are seeing all buttons on the external controller always pressed. See if something is pulling pin 13 of the expansion port (connected to bit 1 of $4016 read) low. Do you have a rewritable cartridge in which you can run a test ROM that I can make for you?
If a game that doesn't read controllers connected to the DA15 expansion port (bit 1 of $4016 and $4017 read) works, but a game that does read those controllers doesn't work, one possibility is that games are seeing all buttons on the external controller always pressed. See if something is pulling pin 13 of the expansion port (connected to bit 1 of $4016 read) low. Do you have a rewritable cartridge in which you can run a test ROM that I can make for you?
tepples wrote:
39 is the strobe.
If a game that doesn't read controllers connected to the DA15 expansion port (bit 1 of $4016 and $4017 read) works, but a game that does read those controllers doesn't work, one possibility is that games are seeing all buttons on the external controller always pressed. See if something is pulling pin 13 of the expansion port (connected to bit 1 of $4016 read) low. Do you have a rewritable cartridge in which you can run a test ROM that I can make for you?
If a game that doesn't read controllers connected to the DA15 expansion port (bit 1 of $4016 and $4017 read) works, but a game that does read those controllers doesn't work, one possibility is that games are seeing all buttons on the external controller always pressed. See if something is pulling pin 13 of the expansion port (connected to bit 1 of $4016 read) low. Do you have a rewritable cartridge in which you can run a test ROM that I can make for you?
Possible to use this test ROM (note: somewhat NSFW graphics) to determine that? I mention this possibility because of the controller rework done here.
Thanks to all of you but especially Tepples for helping me out. It was a short between pin 12 and 13 on the expansion connector (tin whiskers?) that caused the erratic behavour. 
You're the best, all of you!
You're the best, all of you!