Phase Drive Questions

Removed Dropbox links and figured out how to resize my images and insert them, sorry about the nuisance.

I suspect the motion box thing is doing some sort of signal manipulation or filtering.
It seems bizarre to me there's a phase where there's no voltage output. I derive that from the working turbocnc setup I can plug this box into and it runs the stepper smoothly.

There is always voltage applied to the motor,
but as I said, with 2 pins your only real choice
is mode 2.

The driver will create /PhaseA and /PhaseB
from the PhaseA and PhaseB parallel port
signals, so at any of the 4 possible output states
2 motor drive outputs are energized

I think I've found part of the problem. With stepgen 2 I started checking the pin outputs in HAL-scope, and I seem to be getting quite a bit of phase drift on B. A behaves normally but B will run for extended periods and then miss others. once in a while it will synch correctly and run smoothly. I should've taken a screenshot to share. I'm guessing I have more latency then the test showed on this old laptop.
I'm gonna suspend testing this setup until the better PC I have on order shows up.

Thanks for the help guys!