Rotary Table Tuning Problems

Update, I finally got it working, after trying everything I could think of several times I cut the connectors off the cables and soldered them again and to my surprise it instantly worked perfectly. It looked like there was some metallic dust inside some of them. Maybe the way I was testing continuity wasn't finding unwanted continuity.

After trying maybe 100s of times, when it finally worked it was difficult to believe when I turned it on and it is silent. I assumed I must have forgot to connect something. Just to be sure I turned the hand-wheel and the table moved smoothly; what? No way, It moved, it must be a coincidence.
The thought actually crossed my mind that maybe this is a dream and i am going to wake up in a minute.

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Well, there seems to be one last problem.

When the rotary table is moving, at certain spots (always the same spot) it skips ahead about 1 degree, that is about 5 degrees on the motor with a 2000 step per resolution encoder.

I have tried most PID and other variables and it doesn't seem the change anything about the skipping at all,

I am guessing that maybe the encoder has a problem. It is new from US Digital, but I guess it could be defective.

The only other thing that comes to mind is I don't have the index wires connected on the encoder, only A-A and B-B, V+ and Ground. My connector has a problem and I am waiting for a new one to arrive. It seems to update the position on the screen OK without the index wires connected. I wonder if they are read or not for an axis?

Another possibility I guess could be the motor but it seems to run smoothly when the encoder is disconnected. I just disconnect the encoder and turn the jog handle a little and the motor and table turns smoothly..

I don't have a scope, it does look like a fun toy though.

I just discussed this with the encoder manufacturer, he said it does sound like an encoder problem and asked me to send it in.