Comment 27 for bug 1063617

I can confirm Krister's experience, the Flat-file configuration and unity don't play well together and I lost my launcher and all functionality. I moved all my config files from a terminal and started with a completely fresh clean default including:
.compiz/
.compiz-1/
.config/
.gconf/
.gnome2/
.local/

and after login, I set a couple of keybindings in unity settings, then launched ccsm which changed those bindings on its first run, then I selected flat-file config in the prefs and my launcher dissapeared and I can't yet get it back. Apparently, "unity --reset" is deprecated, so I may have to wipe my new default config files again.