So, at my day job, we are setting up a new web server with WordPress Multisite running nginx instead of Apache. For whatever reason, all of the permalinks include /index.php/ and you can’t remove it. If you do remove it, once the page has been saved it’ll be right back on there.
To fix this, you can go into your theme file at the top and add the following:
[code lang=”php”]
global $is_apache;
$is_apache = 1;
[/code]
After adding that, go back to your permalinks page and it should be gone.