Most graphics cards seem to be based around a reference design, so there should be no problems whatsoever.
Unless I'm missing a trick, if a card is PCI-ex compatible, then it should work across the board. I have not seen any examples of Gigabyte not working on an Asus board (for example) or the such like.
In fact, the only time I have ever heard of a probelm was when a friend of a friend bought all the premium components branded "Fatal1ty".... I suspect the board was faulty, but when he drove down to the Abit place, and showed them the set up, he was told that the gfx card was not compatible..... Uh? So get this..... he bought another card from that place!
To this day, I know that his system is not working 100%.... my diagnosis.... a faulty bios.
I digress... my point? Buying all the same brand/licence does not guaruntee that the manufacturer has a 100% manufacturing process and 100% compatibility. Check on the motherboard manufacturers forums if they have one, and check for known compatibility problems, or if there have been a series of problems. If none, then just plum for whatever brand you trust/can afford! Nowadays, even the lower tier manufacturers have some cracking products. The ECS board I have outclocks anything else I've ever owned!