Qt4: Repeat all cannot be set from Preferences
As noticed in: http://forum.videolan.org/viewtopic.php?f=14&t=98696&p=330862
Changes to Repeat all option in Tools -> Preferences (Show settings: All) Playlist doesn't get saved. So if user enables or disables that option via preferences, VLC doesn't remember it.
It seems to be related to Qt4 autosaving, so I would guess the interface saves its current settings when VLC is closed, and the option set via preferences gets overridden at that point.