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A couple of theories
It sounds like there are two issues going on. The first USB problems is likely derived from the USB driver crapping out under high memory load. When a lot of other stuff is running, sucking resources, the dll's that support your connection are more likely to crap out.
I'd recommend ethereal to figure out whether zone alarm is blocking the connection, and/or netstat -a in a cmd prompt window.
Good luck.
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