Check to make sure the PCIe Lane switch for slot 3 isn't turned off.
Also, visually inspect the socket for slot 3, make sure there's no crap on the connectors.
Motherboard: RIVE (3602 bios)
CPU: Intel 3930K @4646MHz
OS Drive: 2 X Samsung 840 PRO (Raid 0)
Storage Drive: 2 X 1.5TB WD Caviar Black RAID 0, 2 X 3TB WD Caviar Red, Kingston V100 256GB SSD
Memory: 64GB G.SKILL Ripjaws Z (F3-12800CL10Q2-64GBZL)
GPU: Gigabyte GeForce GTX580 @795MHz - 1536MB GDDR5
PSU: OCZ ZX1250
Cooling: Phantek PH-TC14PE
OS: Windows 7 Ultimate x64. (EUFI)