so connected a rotary encode to the stepper motor with timed belt
you will need to resolve the quadrature at a very high frequenct since the timing belt connection will give you a lot of 'false reversals'.

Buy one of the Agilent quadrature decoder chips and use it to determine if you have a 'specification problem' or an 'electronic problem'.

You NEED to determine that the mechanics are right before you start fiddeling with the electronics and the code.

If you connected b=dir, a=clock you WILL get erroneous counts from this setup; however I do believe the error is a bit too high.

Just came to think about:
23000 step then count only 13007 pulse of encoder.
is this a constant read over 10 runs or just one run?"

The answer may give the solution. If you get various reads for 10 runs, list thenm all.

Erik