I just explained it to myself while I was in the process of replying that since the nut is out of the picture when you fret a note, how could it affect anything but open strings. The answer is that it changes (slightly) the length of the open string, so that all the frets are in (slightly) different proportional places on the string. This is the same way that an adjustable intonation bridge works, it's just operating on the other end of the string. Since you tune the string open to a standard, it affects every note *except* the open note.
I don't understand this. If I hit a note on the say 12th fret isn't the length of the string going to be 17" (34" scale). How does the nut have any effect on anything other than the open string.
