I set my LVC for 3.2v per cell. 12.8v for a 4S pack. My thunderpower charger assumes that a lipo under 3.2v per cell is overdischarged and charges at a low rate until the voltage gets up to what the charger thinks it should be.

Try setting the charge rate to .5A and see if it will start charging. If it does, let it charge like that for an hour or so. Lipos generally hold their voltage very well and, although 3v per cell is supposed to be the safe limit, getting the pack to 3v per cell means that you really drained the battery.