Charging two lipo's at once???

[BrianG]

That balance plug you have was really meant to be charged through solely without the main leads attached. But, that would limit charge rate to ~2A because the wires and connectors are small. The only way to charge at full 1C rate would be to use the main harness as well, and that's where the problem came in.

Yes, removing one of those common wires should eliminate problems. I say "should" because the charger internal circuits may be bridging them anyway. Best solution is to physically tie the proper balance plug with the proper leg of the main Y harness.