Deffective NES controller ports, have really weird responses....

Ok so I was testing out this NES I bought, I tested it out with the usual Super Mario Bros. / Duck Hunt and I experienced this unusual response... With controller 1, I get no responses whatsoever upon bootup, if I plug the controller into port 2 the game will run just fine.

This is where things get weird, If I select SMB with controller in port 2 and then replug it in port 1, the game will allow me to play just fine, except start and select will not work. I thought I had a messed up controller port, so I inverted their position inside the NES, plugging the Port 1 connector where Port 2 should connect and port 2 where port 1 should normally be. Port 1 works just fine, while port 2 will now give me the same troubles I had before.

The issue must be on board and not come from the ports themselves, I really don't know what to do with this.

As a temporary solution I left the ports inverted so anyone playing single player on this console will not experience any issuesm, even in 2 player games the only downside is that Player 2 cannot pause. I tested things out with a Nintendo Zapper too to see if the ports could play shooting games right, things seemed to work ok but I used a LCD screen to test it off so even if I did see the tv blink when I fired a shot I could not test it properly.

What should I do?

This NES worked great when I first tested it, I did nothing funky with it except straightening each pins of the cartridge connector with an X-acto knife.

 

Check the circuit near the controller ports green connectors at the nes MB. You will notice that there's a pair of protection circuits for each port there. The ones which protect port 1 could be damaged. Removing them (without breaking the traces) won't cause the port stop working but might solve your problem if one of the pins "tripped" the ESD protection.

The chips which do the protection are supposed to self destruct when a electrostatic discharge event (ESD event) happens and thus need to be replaced (they will short out to +5v or to gnd to prevent damage to the NES CPU or the logic chip which help decoding the controller input).

Another suspects are the controller input helper chip (74HC368) or the CPU chip itself (RP2A03) but because buttons work fine under certain circumstances it might not be the case.

But then, in the end the NES control protocol is serial and because of that it's very unlikely your problem would block just the two buttons you mention.

In the end could be that your controller has bad start/select buttons.

 

I'll check these possibilities, the controller does work flawlessly though as I use this exact cobtroller for all the NES I buy so I know it's nit it.
Those are the parallel black bars right?