Hi Paul,
I'm very sorry to hear that but I'm really not pretty sure where is the problem. How are you trying to insert a JS into your page?
Maybe the easiest way for you will be using the JavaScript Web Part:
Javascript Overview.
In other case I really don't see a problem placing the JavaScript directly into the master page HEAD section, .e.g.
<script src="http://your_site/CMSScripts/custom_script.js" type="text/javascript" ></script>
as showed in the screenshot in the
Developers Guide.
Best regards,
Martin Danko