Using FieldPoint to control step motor

I am having problem positioning a step motor. Here is what I am using.
Step motor 200 stp/rev. with a 500 line quadrature encoder
A SS2000D6 SLO-SYN Drive
Field Point FP-Quad-510 for the encoder
FP-PG-522 for the Pulse generator
FP-DO-403 for signals for the SLO-SYN drive
FP-DI-330 for digital input signal for switches
I am able to drive and control the speed and direction of the step motor also display its position. But I am having problem when I want to move a position and stop. I can see the counter working when it reaches the number I want to stop it flys by. If I slow down the step motor way down the encoder moves so low it counts in batches of 2 or 4. Does any one have an idea what can I try or do.

Hello Toro,
It's good that you listed all of your FieldPoint hardware, but which of it is relevant for this issue. From what I can tell, and please do correct me if I'm wrong, is that the FP-Quad-510 and FP-PG-522 is of relevance. You determine the location you want it to move to, and you then start the pulse generation according to the reading from the FP-Quad-510. Is this correct? The problem isn't the quadrature encoder measurements, but the pulse generation.
Does the position change ever stop? How do you currently have it programmed such that it knows to stop at a certain position. There is a command used for the FP-PG-522 which will stop it's pulse generation immediately or on its next pulse. Page 8 of the FP-PG-522 Operating Instructions read:
The Control command supports two actions: Stop Immediately and
Stop After Current Pulse. Both of these actions can stop a finite
pulse train. Stop Immediately stops pulse generation immediately.
The channel goes into the idle state, and, if the output for the target
channel is on, it is turned off. Stop After Current Pulse ends the
current pulse train after the current pulse is finished.
=====
Let me know your thoughts, questions, and comments.
Jared A

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