The website is running on apache and the Rewrite Base is set. I also tested if the .htaccess file is applying and that is the case, the standard SEF urls from Joomla are working fine as well. Any ideas how to solve it?

I've bought and installed JoomSEF for J1.7 on three different website, on two it works perfectly but on the third it returns 404 pages for all links. I've checked the .htaccess file and the rewrite rules, everything is in place but still I can't get it to work. Any idea?