I have been using gnome-session-flashback package for some time now and it has never caused this issue before but i have just got a new machine with Ubuntu 14 LTS on it and when i installed this package it would stop showing desktop icons when i open new instance of File Explorer.
Every time i run this command they show up but disappear when i open file explorer:
gsettings set org.gnome.desktop.background show-desktop-icons true
I also tried setting it from dconf-editor although i think both are same and with the same effect.