OK, here's the thing.
I press Y, I get select + Y.
I press B, I get select + Y + B.
I hold Y and press B, I get normal operation.
All other buttons work correctly. Select itself works correctly.
This is an original console, I've tried with 3 different controllers, all with the same problem. I understand the controllers operate on some kind of data latch/clock cycle. I also noticed that in the clock cycle, the first three states that are checked are respectively B Y Select.
Long story short, in the system somewhere, B is latching Y and select, y is latching select.
I've briefly checked the underside of the motherboard with no obvious results. Next thing I'll try is finding my multimeter and doing some continuity testing. I may be wasting my time, but I don't know what else to do.
Any ideas? Or get a different system?
Thanks.