Amiga 1200 mouse / joystick port problems

[six981]

Hi,
 
I'm experiencing issues with the ports on my A1200. The problem I've noticed is mouse clicks not being recognised. Using port 0, mouse movement and the left mouse button are fine, but there's no response from the right button. Using port 1 and a mouse port swapping utility, mouse movement is fine, but both buttons aren't registering. I've tried a couple of different mice and I've also checked the  continuity of the actual pins on both ports to make sure the sockets themselves are ok. The weird thing is I can access the Amiga early start up control by  holding down both buttons. Can anyone suggest what I should try next?
 
Thanks

[six981]

I've measured the voltage on pin 7 of each port and it's 5v. I've also managed to use a multimeter in continuity mode to trace pin 9 on each port to Paula and pin 6 on each port to the CIA with no problems. That's about the extent of what I know how to do I guess