I recommend maybe power cycling your printer Arduino before printing. Like Illuminarti says, it's probably remembering the position where you last printed and backing back up to the beginning with the extruder and doesn't know that that filament is gone now.
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illuminarti 18
Something about the start gcode isn't working, so that it isn't resetting the extruder position. At the start of the print, it zeros the extruder position, then extrudes a few mm of filamant to prime the head, then resets the extruder position to zero, then starts printing.
The initial 'zero the extruder' isn't working, so that when it tries to move the extruder to its 3mm position (from zero, hence extruding 3mm of filament), it instead thinks you want to go to the 3mm position from whatever position you are at, and so runs the extruder backward to where it was 3mm into the previous print.
Are you running Marlin firmware on your printer?
Can you post the first few lines of a sample gcode, up to the point where it starts the skirt lines?
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