My site is a publishing site, therefor I get the navigation setting on site settings. Update: I made an empty site, and then I activated the features for a publishing site. When I use the publishing template, it worked fine.
But when I change order (I have everything manually sorted) it does not get applied when I save the settings.
The same if I delete the Library / Lists / Discussions from the quick launch and hit save, it will come back once I go back to navigation settings.
(The other settings on the navigation settings is saved).
But when I go to the hidden /_layouts/quiklnch.aspx settings, and delete the items from there, it gets applied. (but it doesn't show the pages).
Why does the navigation not work properly when I make a site from empty and activate publishing features, and works fine if I use the publishing template? Is it some configuration I need to do for it to work properly ?
Update: Everything I do in that controller where I can move up, down, delete, add links, show, hide etc does not get saved (or gets saved and reset).