There is only two real differences between the two ports.
1: the D+ and D- go directly to the Sam3 processor. This should not cause any problems whatsoever.
2: The UOTG support. This support allows the due to supply power to the USB port, instead of drawing power from the port. This is the most likely culprit. If the computer is trying to supply voltage to the USB port along with the due trying to supply voltage to the port, you could get a high frequency oscillation.
The First thing I would do, is to change the USB cable. There should Not be a difference between either port, using a standard USB cable. And if it was a problem with the board, it would make a noise regardless of which port the cable is connected to.
I used different cable and problem is solved, thanks. After this, tried another cables, and still there is no noise. And i tried with an external power source, so not usb, and still there is no noise... But if i insert the first (broken) cable, the sound starts caming again. So, you are right, the problem is in the first USB cable, not in the Board...
And what could make this noise when i insert this USB cable? It is really interesting, and i'm curious about it. Which part can make this high frequency beep or noise?