I've always had AMD CPUs and often with nvidia GPUs, never had any incompatibility problems. And the 5V line actually has 5.10V, it's probably a software issue since I got good readings directly from the BIOS screen, it didn't display 5V though, and that's probably why even gigabyte's software didn't give a good reading for 5V. You'll only have "incompatibility issues" if you want to use 2 GPUs together, aka "SLI" for nVidia and "Crossfire" for AMD/ATI.