Any details from the logs?
Assuming the .htaccess is doing it’s job, I’d guess that Joomla is not expecting what it’s getting, i.e. Joomla is not configured for SEO URLs. I haven’t used Joomla in a while, but I think those settings are stored in the DB, right? If you move your Joomla files from an installation that’s not configured for pretty URLs to a new place, it will still be using the same DB.
In short, ensure that not only .htaccess is working correctly, which I suspect it is, but also ensure that Joomla is expecting the rewritten URLs.