Did you run the truck until it just wouldn't go any more, or did you run it until the LVC reduced the power to the motor? If you ran it until the battery just didn't have enough juice to move the truck anymore, you may have overdischarged the battery. If the battery is overdischarged and you try to charge it, the low voltage will confuse some chargers and freak them out. If you have a dmm or voltage meter, check the voltage of the pack.

I've seen this issue with a couple of chargers where a battery that is under voltage confuses the charger. In this case, and under voltage battery will have voltage too low to be read as a 2S pack, but the voltage is too high for it to be a 1S pack. The charger can't decide what to do and freaks out, then gives its default error, which is a polarity error.

I don't know if the 989 will act this way. It's just what I've seen a couple of times.

Try doing a passive balance on the pack first. Then see if you can get the charger to charge without the balancer in line.