I am using Fancybox for WordPress plugin on my site CoffeeDesignBlog
But as i have upgraded to WordPress 3.4.1, my facnybox is not working at all, i have tested a lot of lightbox plugins and all of them are even not working on my other blog too…Both of the blog are using wp_head anf wp_footer function calls, also the js files for the plugins are also loading…….
Please check any post of my blog and let me know your thoughts about it….
Not sure what the problems are with your websites but had exactly the same thing happen to a pre-production site I’m working on at the mo… Tried a good few solutions but nothing seemed to work…
Finally came across WP jQuery Lightbox (http://wordpress.org/extend/plugins/wp-jquery-lightbox/)… It’s not the prettiest looking lightbox but can be tweaked (it works well with responsive design too which is a bonus)…
Working pretty solid on my WordPress install at the mo (3.4.1)…
Hope that helps…