Yeah both my ipods are like that. But there is a way to get around it. Its dumb, ridiculous how someone thought of it.
You gotta plug a usb device into a second usb port. Then, at least with itunes, you press sync, unplug the second device, plug it back in, and the ipod syncs. Just some weird random glitch, with an even randomer solution. It amazes me that someone thought of that lol.
Mobo audio is fine, unless you do audio editing or have some super expensive sound system.