It seems to me that the categories are no longer working as they used. When using the 'the_category' function. Normally the 'the_category' function creates a link to the category or categories a post belongs to. Now when clicking on that link I used to go to the index.php template and only the posts from that category where displayed, instead I still go to index.php template but all post are displayed (also from different categories). The same happens in the backend, on the overview pane of the post when you click on the category link, all post where filtered to that category, now it's broken and doesn't filter. If you use the filter above and choose a category and click on filter it works perfectly.