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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.
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I could never get the left extruder to work either... I think I tried changing the T0 to T1 commands.
The gpx.ini files has some options for extruders, but mine are all set to 0 (disabled), which is default.
Anyway, let us know if you find a solution.