Check yer routes. http://forum.mikrotik.com/t/v7-1rc1-development-is-released/151250/1
Also hAP ac2 here, MTU > 1500 works fine. Not using VLAN though.
/interface/print
Flags: X, R - RUNNING; S - SLAVE
Columns: NAME, TYPE, ACTUAL-MTU
# NAME TYPE ACTUAL-MTU
0 R ether1 ether 1520
8 R pppoe-wan pppoe-out 1500