well, i have the same problem when plugged into the wall it gets really hot. When its plugged into my PC however it doesn't. One suggestion is to not charge it that way. It wont really damage the iPod but it is not good for the battery. Another suggestion is to drain the battery on the iPod completely and then try charging it again. And last, just don't worry about it but i would strongly suggest draining the battery completely and not charging it immediately after use. Or you could try charging it via a wall plug. But once again it getting hot wont hurt it severely but could damage the battery life slightly.
The wall has more power then the standard USB port, so it changes faster, producing more heat.
Your new motherboard, might have a better output for high powered devices, then your old computer, and laptops usually have a low power on USB, because they are designed to use less power to get better battery performance even when plugged in.
It will probly increase the life of the battery by having a slower charge, but I don't know how much, and by the time the battery start to go, it is time for something new any ways
You can try to turn off wifi and bluetooth, and make sure the display is turned off, but other then that I think the heat it normal.