If the voltage is below 12v (3v/cell) your lipo charger is not going to charge it due to safety concerns. If there is voltage acress the main power leads and its equal to that indicated by checking cell voltages off the balance connector, then its just a matter of getting voltage over 12v so the charger will chartge it as a lipo.
I got a DOA 3S from HC that had a low cell and it wouldn't charge either. I charged it as NiMh until voltage was back over 9v (3v/cell) and the stopped and re-tried charging as a lipo. This time it worked. Use a low rate - I used 0.5amp - you want the voltage increase to be slow and steady. Watch for any signs lipo may be puffing. Obviously stop if it starts to puff and get it outside.
If its just a low voltage prob, it shouldn't puff and you'll wind up charging it successfully as a lipo.