I have read some of the threads on guitar tuning and have not found this particular topic mentioned yet . If it has been discussed forgive me
It is now acknowledged by most , if not all luthiers that saddle compensation alone is not sufficient to guarantee true intonation. For best results, the nut has to be compensated as well. This concept seems ludicrous at first glance. I remember scoffing when I saw an advert for Stelling banjos many years ago describing their compensated nut. Like everyone else (I magine) my first thought was What happens when you put a capo on ?.
However, some months ago I came across an article by NZ luthier Stephen Delft explaining the whys and wherefores of the process, and it was so convincing I decided to give it a try on my own (low-end) Martin, which has never played satisfactorily in tune. The process was long and tedious, and would be expensive if you hired a luthier to do the job (unless you are on Spaw's ass-biting list, he would give you discount rates I am sure). But the effort was well worth it. Previous problem chords like D7 and A now sound sweet and true.
It is worth mentioning here that the reason Taylor guitars sound so true is that they implement a modified form of nut compensation at the factory by moving the nut fractionally forward from the theoretically correct position. They could still benefit from tweaking however. Martin as far as I am aware do not do this (they certainly didn't on mine) and it shows, at least to my ear..

If anyone is interested I will search out the URL for the article I mentioned, or a search for Stephen Delft might turn it up. There has been a US patent granted to Buzz Feiten for this system, incidentally, which to my mind demonstrates the idiocy of the US Patent office. It's a bit like Rod Stewart claiming copyright on "Wild Mountain Thyme" ....

Murray