There’s been reported issues with Intel >=10Gb Ethernet devices on the 2.13rc25 switch firmware. See: http://forum.mikrotik.com/t/css610-8g-2s-in-no-link-on-sfp-with-intel-x520/146985/1
Can you try the 2.13rc12 firmware on the switch and see if that helps? (search the forum for the box.com download links)