GPIO3 & GPIO4 issues for analog inputs

I am still having problems using GPIO3 & GPIO4 for analog joystick controls. I have two Rev 3.6-56V boards. One board works perfectly and the other one does not seem to respond to changes in input voltages as the joystick is moved.

I am wondering if this may be caused by some erroneous configuration settings. I noticed that GPIO3 & $ seem to be hard coded when encoder mode is set to SINCOS mode??? Is this true. Could this be the cause why the ADCs are not responding to changes at the inputs?

Anil Sawe