ISSUE FOUND. I believe the problem only happens when using a SUBDOMAIN.
I tested on a Vanilla WP install using a regular domain (mysite.com)..everything worked fine. Tested on a Vanilla WP install using subdomain (dev.mysite.com) and there we have it, original references to CSS and JS remain.
Confirmed this on 2 separate servers, a VPS & Shared environments.
I've just found a temporary solution: you must enter the ENTIRE URL for the CSS / JS file including the version number (eg: http://www.yoursite.com/directory/style.css?ver=3.5.1).
Obviously in the future you will have to update each line with whatever WP version you are on, but at least for now we have a fix!
Thank You! -
How wold a person get this to work when using a WordPress Network>
(WPMU - Multi-Site)?
Do you have any ideas?