Hello all.
Firstly, for the administrators, I have began by going thoroughly through the documentation/FAQ page and doing a full search through wordpress.org and going through prior posts such as http://wordpress.org/support/topic/mfunc-still-not-working
Sadly, I believe the issue is a bug with W3 Total Cache.
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What I've been trying to do is run a piece of PHP code in my theme's header.php file every time a page is loaded. However, upon turning page caching on the script stops being loaded because page caching is simply just storing an HTML copy of a page thus the php code will not be run, at least to my understanding. Even if I set page caching to ignore header.php it has no effect simply because the page is actually stored under the page_enhanced cache as the actual page-example.html file and thus does not call the header.php file.. I have attempted using the mfunc functions inside of the header.php file but still it does not work. Any help would be greatly appreciated as the page cache does indeed speed up the wait time for loading the web page but this piece of PHP code is critical to be run on every page loaded.