I have the same problem on NenoPi Neo after upgrade to latest nightly build.
Check /etc/update-motd.d permissions:
fa@nanopineo:/etc/update-motd.d$ ls -l
total 28
-rw-r--r-- 1 root root 550 Jun 1 10:41 10-header
-rw-r--r-- 1 root root 6055 Jun 1 10:41 30-sysinfo
-rw-r--r-- 1 root root 436 Jun 1 10:41 35-tips
-rw-r--r-- 1 root root 505 Jun 1 10:41 40-updates
-rw-r--r-- 1 root root 275 Jun 1 10:41 41-armbian-config
-rw-r--r-- 1 root root 253 Jun 1 10:41 98-autoreboot-warn
Then change the files mode and reboot
fa@nanopineo:/etc/update-motd.d$ sudo chmod +x * && ls -l
total 28
-rwxr-xr-x 1 root root 550 Jun 1 10:41 10-header
-rwxr-xr-x 1 root root 6055 Jun 1 10:41 30-sysinfo
-rwxr-xr-x 1 root root 436 Jun 1 10:41 35-tips
-rwxr-xr-x 1 root root 505 Jun 1 10:41 40-updates
-rwxr-xr-x 1 root root 275 Jun 1 10:41 41-armbian-config
-rwxr-xr-x 1 root root 253 Jun 1 10:41 98-autoreboot-warn
There are still some error.
_ _ ____ _ _ _
| \ | | __ _ _ __ ___ | _ \(_) | \ | | ___ ___
| \| |/ _` | '_ \ / _ \| |_) | | | \| |/ _ \/ _ \
| |\ | (_| | | | | (_) | __/| | | |\ | __/ (_) |
|_| \_|\__,_|_| |_|\___/|_| |_| |_| \_|\___|\___/
Welcome to ARMBIAN 5.27.170602 nightly Ubuntu 16.04.2 LTS 4.11.3-sun8i
System load: 0.77 0.24 0.08 Up time: 1 min
Memory usage: 5 % of 496MB IP: 192.168.28.155,192.168.41.99
CPU temp: 40°C
Usage of /: 9% of 15G
[ General system configuration: armbian-config ]
Last login: Thu Jun 1 12:41:01 2017 from 192.168.28.114
chmod: changing permissions of '/etc/update-motd.d/10-header': Operation not permitted
chmod: changing permissions of '/etc/update-motd.d/30-sysinfo': Operation not permitted
chmod: changing permissions of '/etc/update-motd.d/35-tips': Operation not permitted
chmod: changing permissions of '/etc/update-motd.d/40-updates': Operation not permitted
chmod: changing permissions of '/etc/update-motd.d/41-armbian-config': Operation not permitted
chmod: changing permissions of '/etc/update-motd.d/98-autoreboot-warn': Operation not permitted
