Hi Sean,
It looks like the plots would overlay if you zeroed both the command and encoder position before the move so they both started at zero.
I think you have
KStepPresent=TRUE; // enable KSTEP input multiplexing
still set in your INIT Program which tells KFLOP to use bits 2 and 3 to control the multiplexing of the 16 KStep Opto inputs. Remove that and re-boot KFLOP.
HTH