I've to say that the findings of Dan Combine are really amazing, in fact it seems to solve many other start COM3 issues, uploading on other threads.
In my laboratory, there was 3 DUE's which I bought long ago, one of them has been working fantastic but the 2 others suffered from the start up issue or COM3 issue.
Anyway this morning I've soldered 10K surface mount 0805 resistor per guidance of Dan, it is not so easy because bigger than 0603 which I did not have => now this DUE board always work wether to upload, start and many other bothering problems.
Many thanks after all these months or many one year mystery...