Hi,
Yes, following the secuence that you say, the output isn´t correct. The is no problem if the board is not unplugged. If I just close the monitor and open it again averything is fine.
I follow the next steps.
--> Upload the scetch to the board, and open the serial monitor. (Data received correctly).
--> While serial monitor is opened, unplug the Native USB (while powered with the other USB)
--> Plug the Native USB again. Close the monitor opened before(because it is stopped).
--> Open a new serial monitor, and the received data from that moment the data order is wrong.
Like recorded in the video shared before.
No one else has this problem? 
I tried the same with different PCs, 2 boards, and different arduino versions of SAM library.
Thanks for your interest Ard.