I understand all of what you are saying, but to be honest I think it will take more than simple set-up. As I have said before, the nut is not the issue here, as capo'ing the 1st fret gives 'exactly' the same intonation problems, down to the same tuner reading. As it is currently set up, the action is now the lowest it will go without buzzing, the neck is close to straight (0.38mm [rounded] between the bass string on the 7th fret and the fret when the string is depressed at fret 24) all to make sure that the string distance is not the issue. I know it doesn't make sense, unless its the bridge that is the problem...
Oh, and I was wrong about the intonation being worse.. checked it again using a proper tuner this time and its still out but its only 1-1 1/2%... still annoying though....