Main problem, and what the update helped with was for cycling. After charging the battery, the voltage would hold higher than a value programed in the chip. That has been altered, and works great now.
As for under charging, I would double check the cells. Have they been equalized? Are the settings in the t35 set correctly? I use .02 - .03 drop back if over 5.5 amp. and .04 if 5.5 amp. Do they take a full charge on another charger?