I have the same board and the 10Gbase-T ports are misbehaving on it as well. Its nearly impossible to negotiate a 10G link with the switch. It works by chance from time to time, otherwise it either fails completely (most likely) or drop to 1G (if lucky). This is with cat6a cabling of course. If it manages to get a 10G link up and running, it is completely stable until the link is taken down.I then decided to go with what has worked for others, and found this blog post by Major Hayden where he fired up Fedora 23 and got the 10Gb NICs to work. Downloaded Fedora Server 23 Beta but the result was the same. Module ixgbe loads but the link is not active, higher layers fails.
Locking both ends to 10G/Full makes it no better.
I've tested with the driver from kernel 4.2, as well as 4.3-rc7 ("4.0.1-k") and the one that is pending for inclusion in 4.4 ("4.2.1-k", from net-next, which has a bunch of X550 fixes), but no luck.
The times it actually works performance is very good. 9.4Gbps in iperf using 3% CPU, and 9Gbps up/9Gbps down at the same time as well, no jumbos and no kernel tuning. The PCIe warning is obviously bogus, and it also went away with kernel 4.3.
May take it for a spin with Windows in a few days..
Are you using a Zyxel XGS1920-12 switch by any chance?