Yokemad,
Can you post your settings for step charging?
I was also wondering did you do the upgrade via a "real" serial port? or a usb virtual serial port?
What is the "proper" time turn on the charger?
Sodom,
No you will not be able to get full capacity again. You may, in certain cases be able to put more charge into the batteries on average. However, the main benefit would be your cells having longer life, because you can will not over charge any particular cell in your battery pack again.