My Amiga 2000's mouse doesn't work on the first/right port.
Even its buttons don't work but no problem with the second/left port.
Joystick works on both ports though. Anyway to fix it? It's B2000 rev. 6
I have even swapped those two CIA chips but made no difference 
http://phota.me/FA23.jpg
There is nothing wrong with your motherboard, that is the way it is supposed to be.
The mouse only works on the left port while joysticks will work on either port.
The Amiga specifically looks for the mouse on the left port, if you put a game in and set it to single player, it will look for a joystick on the right port, if you set it to dual player, it will look for joysticks on both ports.
You can tell the Amiga to look for the mouse on the right port, but frankly, WHY? if it works fine on the left port...leave it there and don't worry about it.
Dave