I also had a similar issue. My problem ended up being the Visual Composer plugin. It enqueues its own version of prettyphoto that ends up overriding the plugin’s version.
Both versions actually load (because they are enqueued using different names) but the Visual Composer version loads last so it overrides.
I was able to fix this by dequeueing the Visual Composer version in my theme’s functions.php.
However, Visual Composer is a very popular plugin. You should probably figure out a way to make them work together.
