I hope you don't take this as some Mac FanBoy comment, but I have never ever heard of anything like that. How do you know for sure the iPod did that? I can not see any way it could unless it was shorted out in a way it would put a dead short across the USB Ports Voltage and fry something on the Motherboard.
I know you from Anandtech forums and you know I am no fanboy. I see crazy stuff on a weekly basis and never seen anything like this.
Well you know me, and I AM a Mac fanboy
At any rate, I have heard of this happening to 2 other people I know. One on a Dell desktop (2g Shuffle) and one on a 15" MacBook Pro (1g Shuffle). It seems that Apple is having major problems with it, because when you call tech support for iPods, the very first thing it has is a special menu for if you are having problems with the iPod Shuffle.
As far as whether we're sure that the iPod did this, we are sure that it caused the problem. Whether or not it was the entire cause of the problem, I don't know. They plugged the iPod in, it went to detect new hardware, then the monitor went blank and the USB ports stopped working. I built their new machine myself from scratch and extensively tested it to ensure that it would be perfect. Every USB port was tested multiple times, memory tests were run, etc. The machine was absolutely perfect before the iPod was plugged in.
I did some more research on the iPod and discovered that it had a similar problem before. On their previous machine (Windows 2000), it worked fine, but on their work machine (also Windows 2000), it caused the computer to completely shutdown whenever it was plugged in, so they simply used it on their home machine all the time. On their new machine running XP Pro, it caused the monitor to go out and the USB ports to stop working. Very odd...