I installed my Mk3 3D Chameleon on the Elegoo Neptune 2S and it is all setup up and I used the Mk3 Gcode generated and put it into prusaslicer. When I start the print it printed the first color and when it goes to switch the second color it just sits at the wipe tower and does not go to the button location to unload filament so it just unloads and reloads the same color and starts printing again.
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It sounds like it might be pressing the button to fast... Do you hear the pulse count as it presses the button?
It should pulse for each color... So 1 pulse for color 1, 2 pulses for color 2, etc. Are you hearing that?
If no, there is a G4 commands that has a delay in it inside our GCode for each color... You might need to make those times longer.
Bill