ok I've doubled checked the wiring, there is only 6 cables going to the servo, so no built in encoder there. I've also double checked the encoder is connected to the right input on the CSMIO.
I also tried disconnecting the encoder, which resulted in the machine not able to detect move moment of the Y axis so I get a PID error as expected. So I'm sure the machine is looking at the correct encoder, but can't understand why the changes I'm making to the config are not having any affect?