I think these guys cracked it: http://forum.mikrotik.com/t/rb5009-all-connected-ports-flap-a-few-times-a-day/155042/1
My CCR2004+12G also flapped initially when I was setting it up and kept eyes on things - my etherner ports flapped 3 times in 12 hours that day. Each time one block of ports (so six of them) flapped.
Now I keep DHCP table closed unless I actually need it and I never have an issue with ports! And I notice that table kept freezing a lot, unlike any other Winbox menu.