Might be related.
http://forum.mikrotik.com/t/hap-ac-faulty-seriers-very-poor-lan-performance-switch-problem/96655/1
with possible solution https://forum.mikrotik.com/viewtopic.php?f=3&t=106176&start=50#p576065
http://forum.mikrotik.com/t/hap-ac-ethernet-speed-problem/108944/1
with possible solution http://forum.mikrotik.com/t/hap-ac-ethernet-speed-problem/108944/1