For sure GPX alters the Gcode. My start gcode should go from the microswitch (back right) to the front left extreme and wait for temperature. If I use GPX then after back right it goes centre then front left so it does something in the middle of my start.gcode file but I haven't worked out what yet.

It wouldn't surprise me to find out that it changes "current head". I think basically it is brain damaged and needs more development.