Hi Eric, thanks for the feedback! What controller are you running exactly?
I think it might be the addition of the G40, which disables cutter compensation, that might be what you're needing with your controller. I'll throw that into the Inch/Metric posts for the next update if you could try adding it to the beginning of a fresh PixelCNC mach3 G-code program and see if that solves the issue you're seeing.