Hi mac7988,
Do you have interface specifications for the ClearPath Drives?
You might try Open Collector Output Mode by adding 8 to OutputChan0 (use 13,14,15). See:
Step and Direction Setup
You also might try increasing the pulse length as shown in SetStepPulseLength.c
You shouldn't need to Flash anything to KFLOP. To set KFLOP back to the default state Flash "New Version".
Regards