That makes sense, after all (after the initial <10 cycle break in period) the new LiPo is...newer, so it's fast and the cells are balanced better. LiPos have a certain life span, after that they will puff, not take a charge, ect.
Ok then. Don't the more recent Traxxas packs/chargers have their new proprietary main-battery-plug-plus-balance-connector thing, where the main plug is integrated with the balance connector? If so, and you're using an xyz-to-Traxxas battery plug convertor, that wouldn't work. The charger might...
I'd say there's either something wrong with your charger or a battery, do you have any way to check the voltage of the battery? You can charge it best you can then test the voltage, if it reads something close to 4.2 volts per cell or 8.4v for the whole pack voltage, then you're good and it's...