Something strange is going on with one of my consoles. After the console is "warmed up" a few minutes it quits reading controllers correctly. When you press the A button, it pushes A, Select, and Start (or maybe more, but I know for sure it presses those three). It is just the bare motherboard, but I've never had this problem before. I really don't know where to start looking with this problem.
I've tried multiple controllers, reconnecting the stock shielding, Different controller plugs, different adapters. I'm stumped.
If it's an NES or a Super NES, then perhaps the clock signal is going through a poor connection. Have you tried another controller? I had an SN ProPad fail like that: pushing B pushed everything.
Sorry, it is a NES. What 3Gen said reminded me of something though. I have a socketed CPU, as it used to be my copyNES console. Maybe something is up with that?
I'd remove all the chips from their sockets and clean them (The wieman for the connectors works well) and re-seat all the chips. Some sockets are iffy.