As has been pointed out at length in other threads on the subject, there is no such thing as a 'perfect' system of temperament . It's simply impossible to set up a guitar so that all of the intervals are 'pure'. Eventually, as one's hearing becomes more refined, you become more aware of the problems, and the better the instrument is, the quicker this tends to happen. Unfortunately, once it happens there's no way to make the problems disappear entirely. It is possible to minimize them, however, usually by spreading them around a bit, in a manner of speaking, so that no one interval takes the brunt of it. If you never play that particular interval some others can be sweetened up a bit more, but then it can become like the forbidden room in the Gothic novel: you end up going there all the time because you're not supposed to. It's also possible to sweeten things up 'on the fly' by stretching strings a bit as you play, and many good players become quite adept at this.