sorry I am kind of new at this. By trouble I mean that when I tried to change my permalink structure from the /?= to /index.php/etc/etc/ wordpress said the structure was updated, however when you clicked on a new page, category, or post I get a 404 error.
I’m running the site on a windows server, to the best of my knowledge my .htaccess file is write about. However to be completely honest I am not sure about mod_rewrite or how to check it.