The motherboard incorporates a cable diagnostic feature designed to detect the status of the attached LAN cable. This feature will detect cabling issues and report the approximate distance to the fault or short.
I'm wondering if it would be OK to disable the SMART feature to test if that is the issue. I found an article indicating that Gigabyte's driver could be an issue.
My Computer
Computer type
PC/Desktop
Computer Manufacturer/Model Number
Home Built - Jan 2013
OS
Windows 7 64 Bit Home Premium SP1
CPU
i7-3820
Motherboard
Asus P9X79-PRO - Bios 4608
Memory
GSkill F3-14900CL9Q - 16GB
Graphics Card(s)
EVGA GeForce GTX660 - Driver 352.86
Sound Card
On board Realtek ALC898
Monitor(s) Displays
Acer S271HL
Screen Resolution
1920 x 1080
Hard Drives
#1- Samsung 840 Pro Series
#2- Western Digital WD1002FAEX Sata3 Black
#3- Western Digital WD1002FAEX Sata3 Black
PSU
Corsair CMPSU-850TX-V2 - 850 watt (by Seasonic)
Case
Corsair Obsidian 550D
Cooling
Standard 3 120mm case fans, Cooler Master Hyper 212 EVO
Smart Lan is not something that you turn on or off, it's just there and you can use it to test your lan cable. Basically you just select the test now option from inside the BIOS
*Edit
I've just had a quick looky and it seems that Gigabyte have a new SMART LAN functionality on some of their boards to save power.
Smart LAN functionality turns off power to the additional LAN ports when they're not in use.