This issue is on a WP 4.4.2 multisite network with domain mapping and multi-domains active.
After upgrading from domain mapping 220.127.116.11 to 18.104.22.168 sites with multiple domains mapped to them no longer resolve correctly to the domain set as the primary domain in domain mapping.
Several sites with multiple domains mapped to them will only resolve to a different domain than the one set as the main domain.
Rolling back to domain mapping v 22.214.171.124 resolves the problem.
Apparently something was introduced in 126.96.36.199 that prevents the sites with multiple mapped domains from resolving to the domain set as primary.
Can anyone else replicate this issue?