A good start here would be clearing up the confusion between the 'class' file.
Is is a PHP file that generates CSS?
Is it a set of PHP classes, basically one per HTML element?
What code is being spit out into the broswer?
If it is CSS then that usually means that the code is being HTML encoded, OR you have not put the CSS inside 'style' tags. Also, if this is the case then it wont be available to format your links.