I will revive this old post, since I have the same problem:
After activating Joomla's SEF feature and renaming htaccess file all my pages display fine, but my third party extentions doesn't show up or doesn't function properly.
Can't point to the website, since I deactivated SEF (live site) and that wouldn't be any help.
Can anyone shed some light about what should I do so my third party components "listen" to SEF function?