vanduino,
As for the connection issues you see, I'm not so sure. I've had typical issues with long (cheap) usb cables. Also, the Com-USB port translation often gets scrambled on my HPZ620 desktop (Win7). However, I see that with all embedded devices that I toy around with (not just Arduino).
vanduino:
Lowest in frequency, but more distressing, is when the Due locks up during an interrupt event. I have only one interrupt, on a pushbutton, but if the button is repeatedly pushed too quickly, the program freezes. If I push the reset button, the Due reboots but the I2C bus fails (cannot find devices), so all I can do is unplug/replug the USB connection and start over.
Now, the above could be a classic hardware-to-interrupt issue. If the switch connected to your DUE interrupt pin is not properly debounced, then the ringing caused by a switch can send the processor into la-la land. I've seen this several times when attempting to connect a mechanical switch to a hardware interrupt pin, but not specifically with the DUE.
If you haven't done so already, clean up the switch signal (either a hardware debouncer, or clean pulse source), and try again. Because it's an interrupt, debouncing in software will not help.
Good luck,
Chris