SSL Certificate CSR Subject Alternative Names "DNS="

Are the certs being issued from different CAs?

I think most big public CA SSL certs will have the FQDN(one or all) listed completely in the SAN section. The ones I work with do. If the SAN section exists, the clients should be ignoring the CN field. Additionally, the CN field is deprecated, despite current usage, and many apps/browsers are moving to only look at the SAN field.

Good Luck!