Originally Posted by b0uncer
It seems to me that for some reason (unclear to me) you are running Nautilus when XFCE (or X anyway) starts. Running Nautilus causes it to set the wallpaper, put icons on the desktop etc...if XFCE does handle your desktop (saving session really helps), then it's just because Nautilus is ran after XFCE's programs have start up, and therefore it seems like the XFCE session can't be saved. Solution: find a way to stop Nautilus launching when X starts. No idea why you are running it, or what has caused it, but Nautilus should definitely not start unless Gnome is running.
For some reason nautilus was running, and when I killed it everything worked fine again. I must have inadvertently started it when messing around with the trash icon, which doesn't appear be working properly (it won't let me drop anything in it). Anyway thanks very much for this, everything seems OK again, and sessions are saving properly.