In settings I set up permalinks as custom: /%category%/%postname%/
However, for any links to work I must have it set as: /index.php/%category%/%postname%/
It seems that all posts and pages automatically get “filed” as http://www.domain.com/index.php/etc.. I have no clue how to not require the index.php subdirectory. I do not want the /index.php/ in the URLs.
Example are on http://www.bibleornot.org and also on http://stevec828.mysite4now.net/wordpress/. (Note that I installed the new test wordpress in its own directory). On the new test blog the links don’t work unless you hack the URL with /index.php/ after /wordpress/ and before the post or page name. So, on Bible I stuck the /index.php/ in the permalink path in settings, but on the new one I didn’t, but the links are actually built with /index.php/ in the path.