Don't be unduly worried about the variances in the CPU Voltage as this is part of the design of these 9 series motherboards. I have been running the GA-990FXA-UD5 with a Phenom ii 1090T and, at first, I too was surprised by this feature but I have been assured by both Gigabyte and AMD that it is normal and I have to say that it has never caused me any major problems.
The only time it has presented any difficulties is when it came to overclocking but, once again, this is due to the fact that I felt uncomfortable having to raise the CPU VCore higher than I had to on an 8 series board, to allow for the VDroop.