The frequency discrepancy is perfectly normal - a BIOS or overclocking tool can request any clocks they want, but the clock-gens are fixed (something like 26-27 MHz for the core domain on a 260 if I recall correctly) and what is really happening is that the closest multiplier is selected. So, much like overclocking a CPU, setting an absolute frequency accurately is not really possible.
As for the geometry clocks, it's an odd but perfectly way to report core domain speeds - the geometry processing engine runs at the same speed as the ROPs.
They are off by "1 notch" ie 8 and 13 respectively. It's not worth worrying about. And Heaven/Valley benchmarks report wonky clocks on 700 series w/boost, what'cha gonna do.
I think all this info comes over poorly documented I2C buses and chip registers. These programs take their best shot at decoding the information for a large number of cards they can't have possibly all been tested.