For those with issues on the RB5009 with different link speeds (2.5G, 10G, see http://forum.mikrotik.com/t/rb5009-slow-speed-2-5g-bug-report-as-requested/155362/1) it seems they may have reproduced the issue locally and a fix is pending:
We reproduced a similar behavior locally. We are looking forward to improving such behavior with different link speeds in further RouterOS releases.