Last year I worked with BeagleBone Black from element14. I prepared image configured as I need, and burn it.
Burning process was as described here : https://elinux.org/Thread:Talk:BeagleBone_Black_Extracting_eMMC_contents/Flash_unsuccessful
It mean: I downloaded and burned package with u-boot.img and other necessary files which at start up runs script:
echo timer > /sys/class/leds/beaglebone\:green\:usr0/trigger
#un-comment the following line to perform a backup
#dd if=/dev/mmcblk1 bs=16M | gzip -c > /mnt/BBB-eMMC-$RANDOM.img.gz
#un-comment the following 6 lines to perform a restore (be sure to replace XXXXX with your image name)
gunzip -c /mnt/BBB-eMMC-XXXXX.img.gz | dd of=/dev/mmcblk1 bs=16M
UUID=$(/sbin/blkid -c /dev/null -s UUID -o value /dev/mmcblk1p2)
mkdir -p /mnt
mount /dev/mmcblk1p2 /mnt
sed -i "s/^uuid=.*\$/uuid=$UUID/" /mnt/boot/uEnv.txt
echo default-on > /sys/class/leds/beaglebone\:green\:usr0/trigger
But last time I got cards from Embest and that procedure not worked.
When I try to start from SD Card with my image BBB works properly, but when I try to flash eMMC from /boot/uEnv.txt, after flashing I got errors, and message, that system can not find disk.
Last Debian (9.1)image flashed correctly.