It seems it is not a single case of port flipping on RB5009, see this thread. http://forum.mikrotik.com/t/rb5009-sfp-10g-optical-copper-dac-w-intel-x520-da1/153233/13
In my case, my sfp+ interface linkdown at midnight, which clearly indicated it has nothing to do with winbox. Other ethernet interface also has port flipping a couple of times every day.