There is a modified start gcode for using only the left nozzle, but that for the rep 1 dual. its in the start up for the hardware setup for the FFC. I see you have a rep 2. Did you change any of the gcode, i remember someone having issue with start code that came from repg.
I am using a FlashForge Dreamer printer, with dual heads. When I print with the left head, the print is offset left on the print bed by pretty much exactly the distance between the heads. Another way of saying this is that there is no offset applied based on which head is being used to print - the physical position of the *print carriage* is always the same, but the physical position of the printed stuff isn't. If you print with the right head, things are positioned OK. If you print with the left head, you are shifted to the left by roughly 33mm. This seems to me to be a simple omission and a dead easy fix. I haven't tried it, but I'm pretty sure that printing with two colours/materials is going to fail dismally until this offset problem is fixed. One will be positioned OK, and the other (left) one will be shifted left by the distance between the print heads.