Crisis. At least. I tracked it down, with beads of sweat running down my face (the problem were on the production server for gods sake), and the problem were that Panels were in legacy mode and our custom layouts did not work. I found a couple of discussion on drupal.org on the subject. I updated the Skinr module to make panels running normal. Updated the database, cleared the cache a couple of times. And then, finally, everything worked ok again. I could wash my face, and make a phone call to the client to say that everything now was ok.
Lessons learned from this are several, but the most important was - never let panels work in legacy mode