I discovered a conflict with the Lightbox Plus plugin. When activating the "Load scripts non-blocking with head.js (breaks inline scripts)" function, Lightbox Plus stops working. I don't know if it works with other lightbox plugins, but maybe worth to look at.
http://wordpress.org/extend/plugins/cleanerpress/
The javascript loader is know to break other scripts because not all plugins load their js in a standard way. If it breaks, yout best bet is to select exclude jquery.
I've tried that, but still not working. Just leaving the head.js unchecked seems to be the only solution for now.