Might look at the page source to see if something is eating the javascript. For example, the thread tools link to me looks like:
HTML Code:
<td class="vbmenu_control" id="threadtools" nowrap="nowrap">
<a href="/showthread.php?t=152052&nojs=1#goto_threadtools">Thread Tools</a>
<script type="text/javascript"> vbmenu_register("threadtools"); </script>
</td>
The third line is what's causing the menu to be sensitive to clicks (indirectly; the function is defined in vbulletin_global.js). Something like a virus scanner would delete or modify that line; on the other hand, disabling scripts at a browser level would just mean the browser ignored that line.