Cool. So when you tighten up the thru-axle (only in the long setting), it can pull the mech hanger out of alignment. Terrible, terrible design. 
Anyway, according to Giant you have to loosen the hanger (the hex bolt), put the wheel in, tighten the thru axle back up, then tighten the hanger screw back up. Completely backward design, but it should work.
Of course it could be something else, but this is definitely worth checking - it was the only thing that sorted mine. Good luck!