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A week ago, I was trying to add a js script (for adding the snow effect) in my theme html.
By placing it inside the <head> tag nothing was happening but once I've inserted into the <body> everything is working fine.
The script exists as a separate file and I'm using the following code in order to include it
<script type="text/javascript" src="<{$xoops_imageurl}>js/snow.js"></script>
Perhaps this will help you...