Hi Russ,
If I follow what you are doing correctly and the starting Y position is less than 1.0 then the pattern would be exactly like what would be caused by backlash.
Where and how did you check the backlash? I didn't understand what the 80 turns and reference mark were referring to.
Could the drive have a deadband setting?
I don't see where you attached your Init.c program.
What are your KFLOP Axis settings?
I notice crazy Velocity settings in the Trajectory Planner 250 inches/sec. But as long as low feed rates are used that shouldn't matter.
Acceleration Settings are also quite high. Higher than what is specified in KFLOP.
You might consider connecting the encoder to KFLOP so you can observe and plot what the Drive is doing.
Regards