I have not seen that before, but my checkpoint balancer never seems to want to charge thru balance, it shuts off a lot. Most of the time its because its going over 5 amp charge rate, but lately, its been doing it under 1 amp. Personally, I think it should default to charge thru mode, but what do I know.

Because of this, I have also been discharge balancing and then just recharging the packs without the balancer. Seems to work very well, and the packs all seem to stay very close cell to cell. I would get a new one, or borrow a friends and see if they come out differently. keep an eye on the batteries with a volt meter, you might find out whats causing it. If it turns out to be the charger, call Jack at the number on their site. You might have better luck at getting your issue fixed than I did.