An explination may be that the IDE communicates with the arduino USB chip and not a virtual serial port established by the USB chip. If the USB chips have the same identifier, both may be treated as one.
I think this goes back to the rxtx lib. I don't have a problem since switching to eried's patch.http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1237179908
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