W3 total cache cdn url not working with theme

I am currently trying to integrate W3 Total Cache to a wordpress website and i have noticed some rather weird behavior with the CDN url request being sent.

I am currently using s3/cloudfront and i have my CNAME (cdn.example.com) pointing to the cloudfront url.

Now all the images, css and javascript that are not part of the theme are rendering properly with the CDN CNAME url.

example: http://ift.tt/1JlNEXI
http://ift.tt/1yJU42H
http://ift.tt/1JlNEXL

(May I also add that this also happens with the cloudfront url as well.) But when it come to the css and javascript that are part of the woo theme it renders as follows.

http://ift.tt/1yJU42I
http://ift.tt/1JlNEXM

I have taken this up with the theme developers and others concerned but very little has come out from them.

I have looked at various options like using preg_replace to match the occurrence of the weird url and replace it with an empty string.

This however did not work because i was probably using/calling the wrong add_action or add_filter from the reference documentation http://ift.tt/1yJU42L and that of wordpress (I mean wp_head or wp_footer).

As you may have figured out I am not experienced with wordpress and I ask that you please help explain what is going on or wrong with this and possible ways i can resolve this matter.

Thanks for your help.