I am having this same problem and have basically narrowed it down to being a hardware issue, but a little advice would be appreciated.

I built a computer in Aug. and everything was working great for several months. Back in December out of the blue the front USB would shut down the computer when I plug in my thumb drive. This is the first I am getting to look at it and tried a few things to help narrow down possibilities. I plug in a USB extension cable with nothing attached and that shut it down, so I know it is not a voltage problem. I plug a set of headphones in, which shares the header and that shut down the computer. So I now know it has to be a hardware problem.

I opened everything up and the USB header is a block of plastic with sheathed wires coming out so to the best I can see there are no bare wires. I plugged in my iPod cord with the computer off and booted up with no problems and plugged in the iPod and unplugged it with no problems.

The rear USB (the ones right on the motherboard) do not cause the shut down. The mother board is touching the case through the rear plate, where the metal tabs apply pressure. I used brass standoffs and the red washers between the screws and the motherboard, so I think the motherbord should be grounded properly.

I think it is a problem in the header, but if anyone else has any ideas I would appreciate any help.