I think this has to do with the UP2 UEFI firmware, it gives me problem on my UP2 board. I could never figure out what sequence of commands would reliably set the boot order correctly but I also very often see that setting a new entry with efibootmgr looks alright, until you reboot and the boot order was changed (I suspect by the firmware itself). It seems that I have had better luck with adding a new boot entry *and* changing the boot order (efibootmgr -o).
Net net, your installation is most likely just fine but you're dealing with a capricious EFI firmware.
Good to know I am not the only one who got this issue.
Maybe it would be worth mentioning it in the up2 doc section of acrn then.