Hi,
The problem is caused by a 3rd party plugin, which apparently moves the scripts into a loader into the site footer: http://i.imgur.com/oU5B8It.png
This is a known technique, but it doesn’t work with most plugins, just like with related posts pro – because many of them need additional inline scripts to load with the correct parameters. Unless the minification plugin detect and move inline scripts from the header, it’s not going to work properly.
I have fixed the issue by adding a 4 second timeout to the loading script to wait for the main script, but that’s not the most elegant solution to handle this.