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The only Xoops related issue I have had with IE9 is that it clears form data if a module includes a 'back' button. There's some more info
in this thread.I'm not sure from your post whether these are public sites, or on an intranet?. If they are public, I would highly recommend upgrading your Xoops 2.0.9 site as it had some vulnerabilities. AFAIK there are no issues with Xoops 2.0.13, but I would look out for modules that included the SPAW editor. Some versions of that editor were insecure and it was popular at that time.
If you are staying with a PHP-4 web server, most old modules should survive an upgrade to Xoops 2.0.18.2 which is stable and reliable.
The latest version of Xoops needs PHP-5.