Hi again,
Today, I repaired Ubuntu on my Pc, and tried the same setup. It seems to work: The Due is recognised(but only when I use an USB 2.0 port), and I can upload sketches through the native USB with the usb isolator in place. However, after an upload, I have to manually reset the Due, and wait some time before it is recognised again by the Arduino IDE. It seems the problem lies with Windows?(or its driver?).
Since the setup is supposed to work independently of the OS, and the project deadline is almost due, I will convert my code to use the programming port, and hope it does not introduce to much lag.