NES Controllers Partially working

Hey guys, looking for your expertise. I recently took my old NES (original Nintendo) and controller out but am having some issues regarding the controller inputs. The NES is not fully recognizing the controller inputs. Here are the findings:

-Both Controller 1 & 2 behave the same in NES Port 1. Changing Controller 1 & 2 between the Portsmakes no difference

-Swapping port 1 motherboard plug 1 to mobo plug 2 and vice versa made no difference

-On some games where start is not required the controllers work (ie Klax), they work not only on the initial screen but throughout the game. Both Controllers with the controller port in both Mobo inputs (swapped them)

-On Super Mario 1 when selecting Mario/Duck Hunt the DPad & A/B work but on the 2nd screen to select 1 or 2 Players no buttons work - not just Start but Up/Down also dont work.

-On most games on the initial screen Start does not work. There is no ability to use other buttons.

As such I dont think its the controllers. or the port or the connection to the mobo. I think the mobo is the issue (?)

What do you think it is guys and if its the mobo where should on the board should I look?

The mobo is overwhelming and I dont know how they work.I am not an electrical expert but can figure it out with time I think. I got a multimeter to test.

Appreciate your help, cant wait to play some of these games again!