i have had this problem with other IDEs chipkit and Arduino but it is most severe with the DUE. trying to debug a program, connecting and disconnecting the DUE from the USB port and getting windows to make the serial connection is an exercise in madness. works some times, other times i need to press erase and reset many times, unplug replug etc etc. it seems that windows waits a random amount of time to release a serial connection. some times it is a very long time.
i some times need to remove the DUE to connect to the hardware it is running 20 to 50 times a day as i test various code options. i find i am spending more time screwing around with getting windows to make the connection than i spend in programming.
is there some secret that i need to know? is there some hidden registry setting that will release the serial port immediately when the USB connection is broken. or is this just another of the joys of using windows?