Let me help you with this problem you have.
All the information you have provided is very helpful and complete but there are some other steps I want you to try. The BIOS version you posted does not reflect the exact version so I would like you to do the BIOS update using the F7 method.
Here you have the instructions:
Also it is important to mention that there may be a compatibility issue with the card. Have you tested other cards? When you connect a different PCI card besides the dedicated video card what happens?
The update I applied was version 4800 (Latest, release date: 12/06/2011) with the express method (Windows Installer).
I don't have another PCIe cards to check the port, I've only used the PCI (not PCIe) before with no problems.
I'll try the update it with the F7 method and I'll tell you how it works.
Thanks a lot for your help.