Did you use absolute paths? You need to. Also, adding absolute paths to the custom.js will not do much if the links on each page to the menu files are not absolute or at least correct:
Code:
<script type="text/javascript" language="javascript1.2" src="custom.js"></script>
<script type="text/javascript" language="javascript1.2" src="style.js"></script>
<script type="text/javascript" language="javascript1.2" src="menu.js"></script>
Are the above lines, as they appear on your individual pages, pointing to the actual files involved?
NOTE: This is not a solution, just advice and questions. You have not provided enough information for a solution:
PLEASE: Include the URL to your problematic webpage that you want help with.
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