Ok so some more details. I ruled out any networked activated plugin. It's not them or at least, I have other multisite with the same core (akismet/akismet.php, jetpack/jetpack.php, wordpress-mu-domain-mapping/domain_mapping.php) installed which are not having issues. Most of the installs are redirect looping between the main network address and subsite 2. I thought I was on to something until I discovered one looping between the main network address and subsite 12. So no commonalities there. I checked the database all of the following are clean and correct.
- wp_options: options named “siteurl” and “home”
- wp_site
- wp_sitemeta: the option named “siteurl”
- wp_blogs: any entries in the “domains” column that have the old domain name
- wp_#_options: Each sub-site will have sets of tables that correspond to the blog_id in the wp_blogs table. You need to go to the wp_#_options table, where # corresponds to the blog_id, and update the “siteurl” and “home” settings in that table.
Anyone have any other ideas? I'm started to think this might be a bug in core.