Hidden=true?
If user removed a startup item (like iiim) via gnome-session-properties(1), when the item is checked, a customized .desktop file would be saved in $HOME/.config/autostart, with both "X-GNOME-Autostart-enabled" and "Hidden" entries are "true". And on next login, the removed item would not be started by gnome-session(1).
The term "Hidden" is quite confusing, from the "Desktop Entry Specification" and "Desktop Application Autostart Specification" standards from freedesktop.org, we could see it actually means "Deleted",
Hidden should have been called Deleted. It means the user deleted (at his level) something that was present (at an upper level, e.g. in the system dirs)...
When the .desktop file has the Hidden key set to true, the .desktop file MUST be ignored...
