I've seen this on multiple motherboards now of different brands
As you may know, the PCI-E connector is lower in height than PCI connector. Paired with atleast NVIDIA OEMs cards there seems to be an issue where the card can swing ~2 millimeters around sideways while seated in the connector as far as it goes.
No problem you say? Well I've seen this swing result in both total inability to boot the computer and ability to work perfectly fine - until you hit some stressful 3D app and then get random problems from flickering to app crashes and rarely even BSOD. Adjusting
the motherboard alignment (<1 mm change) with the case to make it sit slightly differently has solved the issues but I've never had these issues with PCI or AGP.
I think the problem might be solved if the card was tiny bit (sub mm) thicker or the pins in connectors were slightly modified.
edit - damn can't edit the title, it's not NVIDIA issue if their partners make problematic cards.