First, one small correction: the tp-link TL-SG1008D is a switch not a router though they do perform very similar functions.
I looked at the specs for your motherboard and yes it should be capable of gigabit ethernet. I checked for issues with a FreeBSD driver, there had been some troubles back in 2012 but I'm sure those have been solved, and if you have any connectivity then the driver does function. I believe the driver would be
re(4).
Two thoughts which may not have any consequence but make me wonder. The 'eco/green' reduced power stuff, whether it may ever cause issues. And, have you tested your bandwidth with ONLY the new FreeNAS box and one other destination device? Finally, you said you are sure of your cables and network settings, but I might scrutinize each connector and port to be sure nothing is slightly out of alignment.
Networking tends to be esoteric, ersatz, random, vindictive, or capricious, or any combination, especially when you have to suffer connectivity providers who are rather imperfect and their hardware (which you cannot hardly control). I prefer hardware that does less and requires little or no software but if it needs software and can do more I want it to be something I can control such as an open source solution.
I hope you discover the solution to your difficulty and wish you success.
