The old Comodo certificate signing process for a single domain always produced a certificate with a Subject Alternate Name (SAN). Both www.domain.buffalo.edu and domain.buffalo.edu were included in each single domain certificate. If you requested www.domain.buffalo.edu you would get a certificate for both www.domain.buffalo.edu and domain.buffalo.edu. Likewise if you requested domain.buffalo.edu you would get a certificate for both domain.buffalo.edu and www.domain.buffalo.edu.
This is no longer the case. If you need a certificate with both names you must create a CSR with a SAN field for the second name.