For anything >= 1G base-T you need Auto Negotiation turned on. You can try to force it to 1Gbps on both ports by removing the advertised rates, leaving only “1G base T full” and see if the problem is still there.
Normally this would have been a typical case where flow control could help (traffic coming into a port at higher rate and leaving from a port at lower rate). Here is a recent example http://forum.mikrotik.com/t/bad-performance-with-crs310-8g-2s-in-working-at-2-5gbps/182429/1 Was it enabled on the port of the connected switch too?