We have a similar problem. Our pages all work, and we are using the same custom structure (/index.php/%postname%/) but if you try to comment on our (static) home page, you get the 404. We run IIS6, so I’m not sure this will help us, but it may help some other people:
http://learn.iis.net/page.aspx/466/enabling-pretty-permalinks-in-wordpress/
