Ok,
below my comments :
1) I notice that the statement :
<script type="text/javascript" src="whcookies.js"></script>
is included 3 times in every page.
It should be added only 1 time.
I think you're adding it (2 times) from an advanced theme head_script function, aren't you ?
(1 time is added as I told you above)
Include it only 1 time.
2) I see that you have placed the js in your doc root.
Include it using this syntax :
<script type="text/javascript" src="/whcookies.js"></script>
it should work with the URL scheme that you have adopted ( "/index.php/123/why-do-birds-sing")