Recently, I've been working on a multisite install that had a lot of problems with newly created sites lacking important fields in their table structure. They sometimes wouldn't use the title and email address entered at setup, and would't have any user roles available whatsoever. We traced the problems to the Members plugin and they went away once we deactivated it. Which, you know, sucks, since it's such a great plugin.
The components that were enabled were Edit Roles, New Roles, and Content Permissions. I haven't troubleshooted each one of these but suspect it must be one or the other. That said, I'm willing to help troubleshoot as much as possible, since I have a development site that I don't mind hopelessly messing up. The site is configured like 'site.com/subsite' and not as subdomains, if that helps.