Mill Retrofit with Fanuc DC Drives

I was measuring it against the compliment. I had the probe on channel A and the ground on the probe clamped to the inverse channel A. Same thing for channel B.

Viewing channel a and channel b in HALSCOPE everything looks normal. So I’d assume this isn’t actually the issue either.

You cannot do this without two  differential probes.

Measure the A,B signals relative to ground.

But as you said I don't think this is the issue as long as the position
readout is correct.
 

Measure between gnd and each channel.

Are the motors connected to the linear axis?

This will affect the loop stability

Can you change the velocity loop gain on the drives?

I did have the motor disconnected from the ballscrew initially. I've now connected it back and the problem has not gone away. I've attached a halscope screenshot showing the current status. when i enable the drive it oscillates, starts to smooth out, then runs away. 

I can adjust the velocity loop gain on the drive but i have been hesitant to do that. the drive and motor were working as is with the Fanuc controller before I disconnected them. 

The runaway suggests that possibly  one of the feedback loops is reversed.