I removed index.php from the permalink configuration and now the custom 404 is working.
If I had the option of running linux, I would.. ..but I can’t believe this has been this way for what looks like 3 years now and not been fixed to work better with IIS.
Same confusion for me too. Root directory install. BP have menu items that have /index.php/ in them and …/index.php/members works but just …/members/ does not 🙁