Permissions on rc.local itself are ok.

ls -al /etc/rc.local

-rwxr-xr-x 1 root root 331 Jun 15 01:50 /etc/rc.local

This is the script, to run vncserver after boot - it obviously works fine when ran by hand:

cat /root/RunVNC.sh

!/bin/bash

echo date> /root/rc.local.test

/usr/bin/vncserver -geometry 1440x900 -alwaysshared -dpi 96 :1

/usr/bin/vncserver -geometry 1440x900 -alwaysshared -dpi 96 :2

/usr/bin/vncserver -geometry 1440x900 -alwaysshared -dpi 96 :3

/usr/bin/vncserver -geometry 1440x900 -alwaysshared -dpi 96 :4

And this is what's in my /etc/rc.local. Everything along the way is chmod +x.

!/bin/sh -e

/root/RunVNC.sh

exit 0

I'm on Debian 8.0.