I'd also suggest simplifying things and pulling out the AGP card and only testing the PCIe card first in the various PCIe slots. If it works with the AGP card removed then you know there is a compatibility issue or hardware limitation.
Being pedantic about when it comes to open standards vs open source implementations aside, I am not sure I understand the second sentence or how it really relates or your choice of emphasis in your question.
Can you clarify what you mean?
How she said it seems pretty implied, that the open...