I've experienced the same behaviour a few times on my QNAP 10G port and even detaching and reconnecting the cable physically from/to the port didn't correct it. Reconnecting the cable couldn't turn on the communication and I had to reboot with the cable connected to the port. I haven't checked this with any of the 1G ports.
I should try this once again because now I use the stock QNAP 10G firmware as recommended by @robimarko and see if this happens again.