You dont need Port and Pin numbers set for the spindle in Motor tuning, so I would set them to Zero. Dont think that will be the problem but definitely best to have them that way.
The Jog you mention would seem to be internal in the drive, if that is what you are meaning then it will jog with that method no matter how you have Mach set up, so its not really a good test. Check you have the parameters set correctly for position mode, just had a quick look and PN-00 seems to need set to 2 and PN-01 to 0
I will try and remember to look at the wee lathes setup to double check there is not something needed in Mach.
Hood