I contacted MB Models, and they recommended trying discharging the LiPo, then doing a balance charge, and letting it continue to try and equalise the cell voltages, though it may take several hours to do this.
So, I used the storage mode function on the charger to take each cell down to 3.7-3.8V, then did a balance charge. As before, one cell reached 4.2V and the other cell was still at 4.0V, but I just let it continue charging, checking it periodically to see if the voltage was coming up on the lower cell. The charge current fluctuated between 0-0.3A, but slowly the voltage did come up. It took about 5-6 hours, but eventually both cells were at 4.2V, even though the charge didn't peak and cutoff.
I have since tried discharging 1000mAh from the pack, then another balance charge, and it went fine, each cell reached 4.2V and the charge peaked and cutoff. It appears fine now, and hopefully now that the cells are balanced, they will stay balanced!
