I have exactly the same problem, but with an ASRockRack E3C246D4I-2T board. I updated the firmware using the Intel NVM update tool and now only one of the two ports gets a link. I sent a mail to ASRock to request a firmware update that will restore the functionality, but they haven't replied yet (it's been 2 weeks now).
If you figure this out, please share your solution.
If you figure this out, please share your solution.