Well, this is a mod, so somr risks come with it. It's possible you damaged something. See if another random card, anything even a cheap LAN card ($10), works in the port. If it does, than the problem may be with the card or possibly software config. Try the card in the proper slot and see if it works there, alone.
Now since you say that Windows recognizes them, it may not be a physical problem, but a software one. That's why trying it alone and in the proper slot ( or in another computer) is important so that you verify the card no physical problems.
If it is a software problem, than check your drivers and make sure your settings are correct. Make sure that windows and nvidia (not familiar with them) software all have matching settings and both motherboard and gpu bios settings are proper.