One of the dark secrets of the guitar: guitars don't play perfectly in tune. Actually, all fixed tuning instruments, such as piano, play slightly out of tune.
It is impossible to place the frets on the guitar so that all notes on the instrument will be perfectly in tune in every key -- simply impossible, because of the way tuning works.
There are two basic types of tuning in western music: Pythagorean and tempered. Pythagorean tuning is named after the mathematician who created all those theorems that taunted us in high-school math classes. He discovered the mathematical principles of intonation, such as a pitch whose frequency is twice as high as another pitch is one octave higher. His principles explain mathematically the perfect tuning for each step in the octave.
The problem with Pythagorean tuning is that it works only within one key. In other words, if you tune all the notes on a piano so that the notes are perfectly in tune in the key of C, they will be out of tune when playing in other keys.
Intonation used to cause many problems. For example, in the olden days, when a lute player needed to play a piece in another key, he had to actually move the frets on his lute (lute frets were made of gut for just this reason). Some harpsichordists actually retuned their strings to switch keys.
So, to handle this, a tuning system called "tempered tuning" was developed (maybe it was named after a harpsichordist who got really mad from having to constantly retune). Tempered tuning places all the notes at a slightly compromised frequency to yield good, but not perfect, tuning in all keys.
Tempered tuning applies to guitars as well. The frets on a guitar neck are laid at specific positions to yield a good compromise in tuning, but a guitar can not possibly play perfectly in tune in all keys.
....or.....to hell with all the technical jargon!! by one of these inexpensive tuners...you can set them sharp or flat!! ( 410-480 HZ ) They work very well and are cheap enough that you can afford to keep one in every guitar case ( i do) :wink:
http://accessories.musiciansfriend.com/ ... sku=210527