Torchmate cad/torchmate 2.0 Issues

please help. I have recently purchased a Torchmate CNC plasma. I've used this software before with a previous machine and liked it. But I have a issue that I can't seem to figure out. No matter what I design in torchmate Cad when I Export it to torchmate 2 and import it to cut it. The part either double cuts or overlaps previously cut parts and messes them up. I've made sure that I don't have any play in my x and y axis and checked backlash as well.See pictures for examples. I've tried numerous changes to the files and nothing seems to work. Any help would be appreciated.