I have a multisite environment that has a primary domain (v3.domain1.ca) with a few sites under it (v3.domain1.ca/site1 and v3.domain1.ca/site2), and I used a second domain (v3.domain2.com) in the multisite using the built in 4.5+ domain mapping with a few sites under it (v3.domain2.com/site3 and v3.domain2.com/site4). Using Cpanel the, v3.domain1.ca and v3.domain2.com subdomains were directed to a folder v3 in the public_html folder. It worked beautifully.
This is a development site that will eventually be on the primary domain and not a sub domain, so in an effort to test moving the multisite, I changed the domain to the domain1.ca/v3 and domain2.com/v3 with the subsites being domain1.ca/v3/site1 ... etc. The site is in the folder public_html/v3, so it matches well.
Adjusted wp-config.php, .htaccess, database entries, removed subdomain redirect we are up and running... MOSTLY. Everything on the primary domain1.ca/v3 and subsites front end and admin work perfectly. Th
The problem is on the second domain domain2.com/v3, both admin and front end show correctly. But admin of the subsites domain2.com/v3/site3/wp-admin and domain2.com/v3/site4/wp-admin, both show the data for domain2.com/v3/wp-admin. The link at the top shows domain2.com/v3/site3/wp-admin but you get the actual admin page for domain2.com/v3/wp-admin ... weird. The front end shows a 404 on both site3 and site4.
I've compared the exact structure of the database entries in the working primary domain and second domain and they are the same. I cannot figure out where the settings that affect this are and what would prevent the second domains subsites from now working. Any help is appreciated!