We have 3 web applications in our SharePoint 2013-intranet solution. Two of them works fine. On the third one "sometimes" users get Access denied. This includes farm admin users as well.

After following this tip, the problem is solved (enabling Anonymous auth, waiting, verifying and set it back). But a few hours/days the problem occurs again and its keeps happening.

Anyone have got this or have a clue were to look/compare with the other, working web applications?