[BrianG]

Not sure about the specific settings for the 989, but NiMHs are pretty easy to charge.

Make sure you have the cell count right (if applicable), set the charge rate to about 1C (4.2A). Is there a time limit function on the charger? If so, set it to something like 2 hours so you KNOW you will get a full charge that isn't time-limited. What do you have your delta peak set to? Try increasing it a little. This setting is how much the battery voltage is allowed to drop before the charger thinks the pack is fully charged. You want the packs to be warm at the end of a charge. Hot means the delta peak is too high and could be overcharging; cold means they aren't charging fully.

Charger settings aside, have you ever run the packs until they are less than 0.9v/cell? Are they really hot (>130-140*F) after a run? Either case isn't good for NiMH, especially the heat. Do you maybe have a bad solder joint in one of the packs? One bad solder joint will affect the whole setup since they are in series.