Hi,
Just to chip in had the same issue with libreelec - Nexus on Dell Wyse 5010.
Using General MAD_X64 build you will need to follow these steps (worked for me):
1.mount -o remount,rw /flash
2.vi /flash/syslinux.cfg
add noefi to the line and save
3.vi /flash/EFI/BOOT/grub.cfg
add noefi to the line and save
reboot, after that shutdown work properly and the blue power bottom properly goes off.
Cheers,
Hemant