Please see the following thread:
http://forum.mikrotik.com/t/nv2-thruput-prob-much-slower-speed-than-expected/63839/1
When gigE comes in (especially with NV2) it degrades the effectiveness off fastE devices.
Measuring from/to full 100mbps network is OK. but if the traffic is starting from gigE endpoint (measurement or real life traffic), than speed is only of fraction than expected.
changing all the devices to feed with gigE, solves the problem.
Seems to have backpressure(?) problem? Or gigE want the ACKs faster??