Seems that the color picker eyedropper within RapidWeaver is just slightly off. I don’t know if this is an OS X bug or one specific to RW. If you use the eyedropper to choose a color for a theme variation or elsewhere in RW, like in Stacks, whatever color you choose using the eyedropper will be slightly darker than the color you clicked on with the eyedropper tool. Just noticed it in RW 7, latest beta build, but I’ve had it affirmed for me by other developers that it goes back much further than this.
Did a little digging, and found that this is a problem without an easy solution. RW would need to know the current system colour space, the current colour pickers colour space… It knows it’s own colour space.
Then fudge the result of the pick based on the different colour space variation (seems impossible to me, as you could never for example know anything about a custom colour space like my example image, as I have my system set to).