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MC, I can't say for sure, but it really sounds like you have some USB problems with your computer. If you did choose to root, I would seriously recommend doing it with a different computer, at least until your computer's USB issue is resolved.
I still think it would be beneficial to find at least 2 more computers and play around with the USB issue, to ensure that you've isolated the problem to your own computer. I'm not sure what your time window is on returning the Nook Color, but it would be important to isolate this issue soon.
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