Sometimes you need to reset the default boot option manually, as root inside xterm run this, then reboot. chroot /mnt/initfs cal-tool --set-root-device ask:mmc2 mmc2 is partition 2 on internal mmc3 is partition 3 on internal mmc12 is partition 2 on external mmc13 is partition 3 on external You can also set the default to flash chroot /mnt/initfs cal-tool --set-root-device ask:flash My install-tools does not do this part of the cloning process. Sometimes it works and sometime you need to run the cal-tool