Hi,
I'd look at U975 and the pull up resistors R981-R988. (See page 16 in
https://www.amigawiki.org/dnl/schematics/A4000_Rb.pdf) Check for corrosion or junk on the pins, and see if there's any contamination that might cause shorts.
U975 is a parallel to serial shift register. All eight directional lines from the ports feed to this chip, then Lisa reads the values out over a single line. The resistors set the voltage on the directional lines to 5V when no direction is selected on the stick. When you move the stick, the corresponding direction line is connected to ground.
I'd check the voltage on one of the directional pins of the other port while you do your test. The pin should be a steady 5V as you hold the joystick on the other port. If it drops below ~3V, I'd look for damage around the pull up resistors. If the other port is OK, look for damage around U975, and perhaps replace that chip.
Robert
