When you zero your machine - set it's 0,0,0 coordinate, it sounds like you're setting your Z=0 to the top surface of your material, but in PixelCNC you're saying it's the bottom of the canvas. Try changing your canvas Z origin to 100% (or 0.04") which is the top of your canvas, and keep zeroing your machine the same way you already are. The G0 Z0.14 means that it's .14" above wherever you set your machines Z=0 at. If you want to not have to worry about the thickness of the material then you want to set your project's canvas Z origin to 100%, so that you can set the top of your workpiece as your Z=0. That's the strategy I always go with because it just makes everything much simpler.
Let me know how it goes!
Charlie