7i97T with Mesa CT- Desn't seem to be outputting an analogue signal.

If encoder 2 is assigned to joint 2, then yes, that should be [JOINT_2]

I am being a bit vague because there is no fixed mapping between
hardware=encoder/PWM/stepgen etc and joints. 

That is great thanks mate. Makes sense to me now. Not sure how to tag people in these posts but I'll try inform JT of the issue.