I would think batteries now and days have a safety mechanism to stop charging when its at 100% or near it, and start charging back when its below that. your motherboards software shouldn't have any affect other than charge speed(motherboard vendors love to say they have a special charging software as part of their software driver suites)
lol. I just want to make sure, because apple is replacing my phone. I don't need this problem repeating again, if it can be preventable. It's just the fact that my ipod also experienced one of the symptoms around the same time my phone battery died. This is strange to me; so i naturally thought my computer had done something to them both.