Comment 83 for bug 249373

 This bug persists with me, too: I exited Pidgin, run gnome-session-save, logged out logged in and Pidgin reappeared automatically. (Pidgin is not an entry in System > Preferences > Startup Applications.)
The same result when I rebooted instead of logging out.
uname -a; Linux MD97600 2.6.28-14-generic #47-Ubuntu SMP Sat Jul 25 00:28:35 UTC 2009 i686 GNU/Linux
This Ubuntu version is a dist-upgrade from 8.04.2 > 8.10 > 9.04.
GNOME 2.26.1