I have the same problem with the 2.5g port but in an opposite configuration. I made my own post about it:
http://forum.mikrotik.com/t/rb5009-2-5g-port-problem/155768/1
In my configuration my WAN port is on a 1g port and my computer is on the 2.5g port on LAN bridge. Since my setup is opposite, my lower speed is on upload rather than download which indicates that the problem is 2.5g port sending. My behavior is exactly the same, if I remove the 2.5g advertisement and force the computer to connect at 1g my upload speed returns to normal. By the way my computer on the 2.5g port has an Intel I-225V NIC built into the motherboard.
I also had another problem with the 2.5g port that I’m not sure is related but may be. I noticed that at 2.5g if I upload large amounts of data to the internet (this occurred during my nightly remote backup), the 2.5g connection would go down. Windows would show a cable connected but no internet, renewing the IP address hangs forever, can’t ping or connect to anything. All other devices on the RB5009 were fine and had internet, just my computer on the 2.5g port loses connection and never returns. Only thing I found that fixed it was to reboot the PC, never had to reboot RB5009 to fix it. It seems like this is a related problem because it only occurs when my computer uploads large amounts of data, downloading had no problem. Since removing the 2.5g advertisement and running at 1g, I no longer have this problem. For this reason the 2.5g port is unusable at 2.5g to me at the moment which is disappointing.