No it is not bad. You will loose about 2% of the cards performance max because of that. The other question is what CPU do you have and is it able to keep up with the card?
So where did you get a board that supports FX and is only PCIe x16 ver 1.x? All AM3+ boards are at least PCIe ver 2.0. Unless you have one of those N68 boards that nobody should buy.