I just had a stupid problem, had a drupal installation in subfolder and there is much info how to solve this on the official clean-url page, but this problem isn't there. Sometimes when you copy files to windows and then copy it back to linux .htaccess will lose it's dot and then clean-urls and something else might not work but you won't notice it because you don't look for it. So check if file has a dot and check if there is a file at all, this will cause you 500 server errors if not working right and you have clean-urls somehow alread enabled or have static links (maybe you had a test site on one server and then moved it to other).