Your post is a little confusing....the charger has a safety thing where it will not charge if voltage is below about 3v/cell, so if the 3S doesnt have 9+v, the charger won't charge it.

Where you said "cell one=1.9, cell two=1.6, and cell three=1.5" - that doesn't come close to 11.6v (or 9v for that matter).


What does the voltage across the main power wires read for both 3S lipos?

If the voltage is greater than 9v and the charger is not seeing the 3rd cell and you have it setup correctly and the balance connection is correct, then it sounds like there is a prob with your charger.

Are you sure the balance connection is correct?