Extruder lengths keep changing

I added an new extruder to my MakerFarm Pegasus 12 as the old ones cover cracked and warped a bit and it seemed as it wasn't extruding correctly. I replace it with a clone and found the follow issues when setting up the steps. My issue is not the extruder as I thought at first.

I used Ponterface to set the steps. I started off with the original steps listed only to find out I was short. I then changed the steps and then I was way over extruding. After many tries I was not successful. I would go back to the original number only to find a different length extruding compared to the first time I used that number. Problem solved it was slipping, but no that wasn't the case here. I removed the cover and removed the tension rod and just kept the plastic gear in place with the motor gear and marked the gear to see how much it turned each time I ran a test. To my surprise every time I change the steps from 660 to 700 back to 660 the gear would stop at a different point from the first time I ran the 660. What ever extruded the first time at 660 should be the same after I change it back. I am confused wondering if its the motor, Marlin or Pronerface. I did check that the numbers are correct each time on the printers interface. HELP


Example to be clear:

660 length extruded 8.2 mm
700 length extruded 8.6 mm
660 length extruded 7.4 mm

I just ran another test using just the printers interface to adjust the steps and pronterface to extrude and the same thing happen.