I'm using the Boilerplate theme, and although wp_footer is present in the theme and other plugins (SEO Platinum) fire correctly, JetPack nor WP Stats fail to deploy. I can see in the code that the call to the JS file never gets output onto the page.
So something is clearly wrong with this theme's wp_footer function. It's not getting messed with in the function.php or anything....
My question is: what can cause this, how should I go about debugging?