No Programming via Native USB port possible on Linux

Official Hardware Mega Due
6

Now it becomes totally weird. It seems that the device needs up to 20s to come up. Look at this. I tried bossac every 5s:

$ stty -F /dev/ttyACM0 1200 
$ /opt/arduino-1.5.6-r2/hardware/tools/bossac -i
Auto scan for device failed
Try specifying a serial port with the '-p' option
$ /opt/arduino-1.5.6-r2/hardware/tools/bossac -i
Auto scan for device failed
Try specifying a serial port with the '-p' option
$ /opt/arduino-1.5.6-r2/hardware/tools/bossac -i
Auto scan for device failed
Try specifying a serial port with the '-p' option
$ /opt/arduino-1.5.6-r2/hardware/tools/bossac -i
Auto scan for device failed
Try specifying a serial port with the '-p' option
$ /opt/arduino-1.5.6-r2/hardware/tools/bossac -i
Device found on ttyACM0
Device       : ATSAM3X8
Chip ID      : 285e0a60
Version      : v1.1 Dec 15 2010 19:25:04
Address      : 524288
Pages        : 2048
Page Size    : 256 bytes
Total Size   : 512KB
Planes       : 2
Lock Regions : 32
Locked       : none
Security     : false
Boot Flash   : false

As you can see. After 20s I get a connection. Huh??