I'm not sure what may be causing this problem. I put it under domain mapping because I just updated the plugin today so I don't know if it is causing the problem or not. If you try to login to a subsite, you get a 404 error. Right now, the only way to login is to go to the main blog - but my subsites have never been instructed to login from there.
I am also in the process of converting to https. I am finding that I cannot access the subsite dashboards from the super admin dashboard as normal. It is requiring a login and then I get the 404 error!