If the PCie slot on your motherboard accepts other cards and the system can POST, then the slot itself is not faulty. If the graphics card allows other systems to POST and works within the OS, then the graphics card is not faulty.
That leaves a possible compatability issues that may be related to pullup resistors on the presence detect logic (within the card or mobo?) causing some PCie/BIOS configuration issues during POST (causing POST failure & black screen).
If your POST failures are related to such presence detect logic failures, it may be solved by forcing the presence detect logic to a specific and desired lane count, either x16 (16 lanes) or x8 (8 lanes) or even x1 (one lane).
Such issues/solutions have been floating/discussed on the web for some time. They have even been discussed on the workstation forums and one such forum post is here. There are more related threads on the workstation forum but they can be difficult to find without knowing what to search for ;)
[edited to add the following]
Oh, and if BIOS has indeed fixed some POST or PCIe compatability issues via some update, there should be some mention in the BIOS release notes. If there is no mention, don't expect that a BIOS update will magically resolve your problems. And as you have issues even performing a BIOS update, don't frett, simply read the release notes and you may find that the latest BIOS has some prerequisits (like a certian BIOS revision for the update to succeed). So read the release notes for all BIOS releases and you may better understand why there are problems.