Mill Retrofit with Fanuc DC Drives

I just tried increasing D and it seemed to increase the amplitude of the oscillation as I increased the value. 

I also wanted to verify the encoder is working correctly even though it appears to be working correctly in halscope. I hooked it up to an oscilloscope and got a chart I wasn't expecting. Channel A seems to be stopping at 0V on both the rising and following edge. channel B seems correct and bounced between +5V and -5V.

Would this cause any issues with counting on the mesa card?