Seems so that there are more threads with that problem.
I had started one: http://forum.mikrotik.com/t/strange-limit-to-throughput/87608/2
Found also this: http://forum.mikrotik.com/t/6-29-1-internet-speed-drop/88863/1
So there is a general problem with newer versions of RouterOS.
I hope the guys at Mikrotik can look into this.