I found part of my problem today. I had a broken wire at the encoder connector I made. I guess I nicked it when stripping the outer jacket off the cable. When I bent the cable to fit under the cover, it broke. I was able to solder it together.
Looking through the Gecko start up procedure, I noticed that I would have to remove the drive to remove the cover to get to the test points. I decided to just wing it again. This time when I powered up the Gecko it was trying to hold the motor still. After a lot of very fine adjustments, I was able to get the drive tuned enough that the motor would stay in position no matter how hard I tried to turn it, and without growling and loosing steps.
But, another problem cropped up. I think my DB25 cable is not a straight through cable. I could not see any step signals on my scope while mach was commanding a move. I also had other ouput pins active that should not have been. On the way home I stopped off at a computer store and got a different DB25 cable. Hopefully this one is a straight through. I will check them both tomorrow, pin for pin.
Vince