I use nitrogen
to set a different wallpaper for each monitor. It requires disabling of the Nautilus desktop, but works great. Until I reboot...at which point the settings are lost and I go back to the default Gnome wallpaper which is the same on both monitors.
Anyway to make the nitrogen settings stick?
You add nitrogen to your commands to run at log in
How to run commands at login on ubuntu 12.04?