Need to make sure the voltage is being indicated correctly from the balance plug. The charger uses that to decide if lipo is below safe level to charge which is usually about 6v. If balance connector is messed up, charger is seeing one cell as 0v which it may not really be. Regardless, the 0 and 3.8v from teh other is not above the safe charge level so the charger won't try and charge it.

Fix the balance lead and if you have a dvm, check the voltage yourself from the balance connection and see what voltage is for both cells. I doubt you've pulled one cell to zero - it would have puffed on you going that low. Need to fix the balance wiring and try charging again.