Originally Posted by giulix
Delete the saved session: System->Preferences->More Preferences->Sessions, click on Default (I think it is) and press Delete.
Thanks, that did get rid of the Nautilus window while still letting Nautilus draw the desktop.
Alas, it also got rid of Firestarter and GKrellm, and as soon as I saved the session with those running on logout, the bleedin' Nautilus window was back the next time I logged in! Argh.
In case anyone else gets this problem, this finally worked for me:
1. Delete the Default session as per giulix' instructions.
2. Add what you want to run in the "Start-up programs" [translated from Swedish] list in gnome-session-properties. Click "Close". Do NOT touch anything else.
3. Again, do NOT touch anything in session properties. Do NOT use "save session on logout". Forget about trying to change the starting order for your programs, their rules for re-starting, or anything else, it will force an open Nautilus window upon your poor desktop at every login.
Conclusion: Either Nautilus or GNOME's session management is b0rken?