I would highly recommend trying a few different post processors. I had to experiment with that a bit before I stumbled on the secret sauce, so to speak. Try the post I mentioned above with WCS set to 1 (the probe WCS will also update to a 1, which is fine).
Do you have limit switches setup and/or are you homing before each job?
Another thing to check is that there aren't any large Z moves in the positive direction (up) at the start of your g-code file. The machine is dumb and just doing what it's told, so there's likely something right there near the top that's creating the behavior you described. Feel free to post the first 100 lines or so of the file and we can probably spot the issue for you.