Linking JavaScript Query

When linking to a JavaScript file I am including the following in the 
html.head template in
my customization:

<script type="text/javascript" src="../xhtml-javascript.js"></script>

When my xhtml chunk stylesheet completes its job, this line is 
converted to the following:

<script type="text/javascript" src="../xhtml-javascript.js"/>

This is nice and tidy but my browsers are not liking this and the pages 
will not appear. If I
manually edit them back to what I placed in the customization, they 
will appear when refreshed.
Is there a way to control this empty element cleanup to preserve the 
script end element?