Same thing is happening to me right now. I opened a thread about it. http://forum.mikrotik.com/t/dns-forwarding-is-not-working-anymore/149552/1
Looked those 2 as well.
https://www.reddit.com/r/mikrotik/comments/g0gr3n/dns_requests_to_pihole_still_struggling/
http://forum.mikrotik.com/t/dns-redirect-using-nat-adding-vlan-issue/128882/1
No luck, but now I know its due to the VLANs, implementation maybe?