Thanks for your quick reply and update!
If I may give another remark, the fancybox js file is loaded in the footer (which is great :)). The custom js script for adding the classes and starting the fancybox is loaded in the head, which caused issues because we load jquery in the footer as well.
We added jquery in the head now as a workaround, but maybe there are other options? (load the script with the wp_footer hook?)
Cheers,
Frank