Yeah, you'll be fine as long as you don't have a VIA chipset... lol. I believe quite a few of those had trouble with 38xx series ATI cards w/ no BIOS / driver updates released.
Anyways, PCIe 2.0 just expands the bandwidth of the current x16 slots. That being said, no card currently released will even use the entire bandwidth offered by PCIe 1.0a / 1.1 slots. So you've got nothing to worry about.