Marked - 12:09 am on Dec 17, 2012 (gmt 0)
I found the solution in PHP. The PHP framework I use (called Hydrogen) relies on $_SERVER["PATH_INFO"] to load various controllers. Using FURL's, on every page $_SERVER["PATH_INFO"] always equaled nothing. It needed to be set to the same thing it equaled when a url was loaded that included /index.php/, which on my host is simply:
This one line solved the issue for me. Phew.