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Yeah, it sounds like the USB headers might be plugged in wrong. It's very easy to fuck'em up if they are the seperate positive and negative wires that go on the motherboard. Getting 10 of those on the motherboard correctly is tough. Some motherboards have those USB headers that are all built together so you simply plug it in with no problems (VERY convenient). If the motherboard has the built-together USB headers, then I'm not really sure what the problem could be (you can't really plug them in wrong).
Maybe you need to install the USB drivers for the motherboard in Windows? The USB ports on the motherboard near the chipset are different than the onboard USB near the keyboard/mouse slots. I'd check Device Manager and see if anything has a yellow exclamation on it. If it does, I'd try to update the driver automatically. Oddly enough, this fixes problems like the USB issues many times.
-Lasereth
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"A Darwinian attacks his theory, seeking to find flaws. An ID believer defends his theory, seeking to conceal flaws." -Roger Ebert
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