I've three arduino DUE boards and check all resistance on each, roughly R3 R14 R15 R21 and R23 have 1K value so I don't think the root cause is these resistance, there must be something else maybe a capacitor I suspect.
Why: all my 3 boards do have same resistance but only one does work when downloading a sketch.
In fact, sometimes it will upload ok, I'd estimate say 1 time it flashes CPU over 7 times ail it will not see the port of my MacBook Air.
The other problem to be honest, i've written Federico and no response, this thread has been lasting so the question being if arduino wants to solve the issue !
If downloading via native then it will work always