Guys..... There is of course a simple answer to all of this.... It's obvious that this is a MOBO Fault.
This was kinda funny to read, given the multitude of things it could be, and the statements up to that point that didn't definitively rule out other things. To me, this could be a driver issue, since it's happened to me as well, and that was the problem.
Just because XP has a built-in driver for it doesn't mean it's the PROPER driver for it. When building a new PC, it's common that one of the first things to do after getting the PC operational (with OS installed) is to go online and update all drivers. Manu-specific drivers may have been written specifically because XP's native driver(s) cause such wonky behavior.
The solution I was given (and I think mine was a Gigabyte board as well) was the same as all old USB devices as well as cameras. Remove the ports from device manager, go into the case and unhook the header wires. Reboot. Run the mobo disc and install the drivers (hopefully they'll be recognized, otherwise....different steps). Reboot. Reattach the header wires, check device manager to see no exclamation points....off you go.
I have no idea if this could work or fix your problem, but there's fistfuls of info out on the 'net for exactly these problems, so you're not unique or alone with this, and as you've found out, it wasn't obviously a mobo problem. One thing - someone brought up manu's cutting corners to save costs...the case you switched to, was it a DIFFERENT TYPE of case, or just another copy of the same case? Perhaps you're a victim of such cost cutting measures too.