Thanks for all the tips. I am working on this for the third day in a row, I am leaning toward a noise issue for now although a few questions remain.
I had been meaning to replace my Bob Board for a while since the speed control I was using was a little flaky (CNC4 PC patched in trough the Bob) and I had PMDX board sitting around waiting for a different project. I wanted to rule out any damage to the board so I went ahead and did the long task of swapping out the entire board. I also swapped the encoder from the Y and Z to rule out any encoder issues. I have already ruled out damage to the Gecko as stated before.
That seemed to sort it out pretty well at first. I was running tests, running the Z up and down at various speeds and it seemed to be holding tight. So I thought I would try and turn everything on, lights and Fans and the Spindle and run the test in a working environment. Then I started getting the same error again. all be it a much smaller error than I was getting before.
So I started tying back wires and just making sure any higher voltage cables were as far from the encoder cable as possible. and continued to test. I have basically narrowed it down to the Spindle. If I run the spindle. I get errors. If I leave it off, seems fine.
The encoder wires are shielded so I am not sure why I am having this problem all of a sudden. I have used this machine without issue for years. Is it possible for a lightning strike to cause shielding issues??? anyway, I am not really sure how I would go about shielding the encoder from the Spindle motor if that is what is generating the EMI. They are in reasonably close proximity (say 6" or so) Since the motor is on the Mill head and the encoder at the top of the Z column. But again, why all of a sudden. I am racking my brain to figure out what else is different in this picture.
Any thoughts?