i worked out what was causing it. i had my scripts like the following. as i simply copy pasted out of the basic html website im porting.
<script language="javascript" type="text/javascript" src="filepath/script.js"></script>
doing this causes no javascript code to work on any pages other then the index page.
to fix it i simply looked at the whmcs default script calls and changed mine to look like them and woola it fixed it.
<script src="filepath/script.js"></script>
that was a nice use of 3 hours or so reading everything working out wtf i was doing wrong while working on other stuff. major facepalm.
oh well its all in the learning i guess it happens when ur learning php, js, html, css on the fly, on a need to know basis lol.