RE: dumb me/electric
Sounds like your charge just has a flaky balance circuit. My Accucell 6 and Venom chargers will charge any of my 2cell and 3cell packs in about an hour, and I usually run my packs down until the esc low voltage cut off kicks in. You might try buying or making an adapter and charging two packs at once as is if they were one 6cell pack. Just a thought, don't know if it would make a difference in charge time, but at least you would be charging more than one pack at a time. You might experiement with your charge settings, hook up a watt meter or amp meter in series with the main power lead to the pack and set the charger at 1amp and see what it actually delivers. Then you might monitor each cell individually and see what's going on.