Stylesheet changer not working with WP links

Hi, I hope all this makes sense…

I have just installed a WP blog to use on my website, as a function on my website I use a stylesheet changer written in PHP so users can change the text size, I wanted to integrate this into the blog. I have partly done this, when I use a self written permalink the cookie information on which stylesheet to use is retained however if I click a PHP link integrated into WordPress (e.g. a category link) the cookie info doesn’t work. I don’t understand why this is. Any help is much appreciated.