This has been confirmed by some users on the forum if it's what you want to 
know.
http://ubuntuforums.org/showthread.php?t=568995

If the autostart file is doing is job despites the presence of the item in the 
session file then this is not an issue but more an unusual way to handle this.
I mean that i already checked that items unchecked in the session setting 
window are well put to X-GNOME-Autostart-enabled=false in the corresponding 
.desktop files (which BTW are not recognized in nautilus for weird reason).

Anyway it's been a long time this bug report has been posted and i don't
have time to test things anymore for the moment so maybe this bug report
can be closed as i won't be able to provide you more information than
the one i have already provided in the near future.

To conclude this bug seems a bit painless for me and i would have really
preferred that the other one i have reported about gnome-session have
been answered and fixed has the problem is more serious and the fix
simple.

Thanks you for your interest.

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system > preference > sessions unchecked items still appear in session file
https://bugs.launchpad.net/bugs/162831
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