Arduino due can't exit from bootloader mode often

_From @sined23 on April 3, 2016 11:59_

Hello! PC is connected to Arduino Due by Native USB. Often after sketch uploading through Native USB or when I plug usb cable or after OS restarted (power restart), Arduino Due still keep in Bootloader mode and usb communication with PC doesn't work and sketch doesn't work.
After hardware reset of Arduino Due it become normal.

lsusb | grep boot
Bus 001 Device 020: ID 03eb:6124 Atmel Corp. at91sam SAMBA bootloader

I run manually bossac's command to reset Arduino Due but it doesn't help:

~/.arduino15/packages/arduino/tools/bossac/1.6.1-arduino$ ./bossac -p ttyACM0 -R

lsusb | grep boot
Bus 001 Device 020: ID 03eb:6124 Atmel Corp. at91sam SAMBA bootloader

Why can't Bossac reset CPU? Is this bug or need send some additional command to CPU to reset?

BTW: Arduino Due can recieve new sketches but can't be reseted by Bossac.

_Copied from original issue: arduino/Arduino#4805_

Reproduce the failure using the Arduino Due Native USB connection and the shown bossac command against ttyACM0, checking lsusb for the SAMBA bootloader state. Compare the behavior before and after a hardware reset, then determine what makes bossac -R fail to return the board to normal sketch execution; done means the board exits bootloader mode reliably after upload, connection, and restart.

Written by the indexing model from the issue text.