Ok, just want to finish what I began. I tried the card in both ports and both work fine. So no problems.
I RTFM and it didn't help, thats why I posted this thread. I went to the gigabyte website for the PDF and it didn't state it either. I actually found that the Gigabyte manual and PDF were pretty poor at actually answering any questions I had , the information was just to brief in description. I also had to update the bios to id my cpu correctly but gigabyte provides little information on their bios updates, I had to find all the info from the community sites and forums such as here.
Anyway thanks to those who tried to help.
Matt