I have been using Drupal for a loooong time and I have never seen this I woke up this morning and my theme was a mess (clearing the cache pulled it back) but my 1st primary link which linked to a subfolder containing php link directory now points to my theme css file www.mychemistrytutor.com/gamma click chemistry directory
So your problem is when you click on [Chemistry Directory] your entire theme doesn't show up? Have you set it to a default theme to see if the error reproduces at all?
i probably seem crazy now Drupal somehow cached a broken version of my site, after clearing its cache and then the browsers it cleared up but it must have been broken at least for a minute to cache in correctly