Every time you change something are you rebooting a few times before deciding it does not work? The OS can cache stuff and even though you updated files it could still be loading Old setting. But it appears like you are going to need a custom SSDT to properly inject the ports on your card. Alternatively you can try and return and get a sapphire card or a Reference card. In my first post on this thread you will see that I also had issues with the gigabyte though I do not remember having issues with the ports.
@pastrychef might tell you that your cables could be the issue.