codegene on "[Plugin: W3 Total Cache] Minified js moves to bottom if I exclude certain js"

Initially when I select auto minify, all minified js and css are in the head tags. But if I exclude certain js from minify, then the minified js files move to the bottom which breaks the functionality of certain plugins since these js files are required to be there in header. How to prevent the js files from moving to the bottom?

http://wordpress.org/plugins/w3-total-cache/

http://wordpress.org/extend/plugins/w3-total-cache/

<---Sorry. Posted this question twice by mistake. Please delete this duplicate thread--->