This sounds like lost steps, and probably has little or nothing to do with DeskCNC. Many people experience this with stepper systems.
Check that your machine returns to the original position after the completion of a program. If it does not, chances are you are attempting to over drive your steppers ( too fast max velocity settings). Slowing down the max feeds and rapids and/or extending the acceleration time by increasing the scale factor will usually cure the problem( backoff maybe 15-20 percent max).
If you have to backoff too much, you may have the driver interface or motor connections setup so that noise is affecting the accuracy. You need to have step, direction, ground and +5v connected for most stepper drives to function correctly.
Your problem is most likely an electrical or configuration problem as the DeskCNC controller produces a very precise and noise free step and direction signal.
Fred Smith - IMService