Hi Dan,
Yes I think that would indicate noise being introduced into the KFLOP/Kanalog GND and affecting the Step/Dir signals. It sounds there might be a ground loop problem. Grounding is very complex. Its hard to make suggestions without knowing all the details of your system's components and all the Grounds (DC and earth) and what circuits are isolated. Are the Viper Step/Dir inputs isolated? Can you describe the Step/Dir wiring? Shielding? What mode are you using (LVTTL or open collector)?
Kanalog Analog Outputs share a common DC GND with KFLOP (not isolated). KStep has one Analog Output that is isolated. You might consider using that. It isn't as linear or as high resolution as the Kanalog Analog Outputs but works well for basic speed control. So that is an option you may consider.
HTH
Regards