Hello,
I have also the problem guidol has run into for a long, long time.
Reboot doenst work. I have to "shutdown -h now" and then power-cycle.
The weird thing i run into is, the system boots just every 2. time from emmc into armbian.
I have then to boot from sd, "shutdown -h now" and then power-cycle and the next boot, boots into system from emmc.
For me, it is a work around but not very comfortable.
Regards
Cyber