Public bug reported:

Binary package hint: gnome-session

To reproduce the problem under Ubuntu Lucid:

1. Login
2. Open Gedit
3. Modify a file and don't save
4. Logout or shutdown

Now notice that you see both a Gedit would you like to save window and a
"Programs are still running window."  It seems that the "Programs are
still running window" should not appear until after Gedit has asked you
to save and close.  If this is not the case, then why do you get to
notify the session manager that you would like to interact with the user
with gnome_client_request_interaction and gnome_interaction_key_return?
This is especially bothersome since the "Programs are still running
window" appears second and tends to cover the Gedit confirm save window.

** Affects: gnome-session (Ubuntu)
     Importance: Undecided
         Status: New

-- 
Pops up "programs still running before waiting for programs to interact
https://bugs.launchpad.net/bugs/605966
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