Achieving perfect intonation on guitars is challenging, even with adjustable bridges. Here’s the deal: a guitar’s 12th fret is theoretically located halfway between the nut and the bridge, creating the octave note for the open string. The problem is that pushing the string down to contact the fret stretches it slightly, making the note go sharp. Most guitars compensate for this by moving the bridge or adjusting the bridge saddles back slightly.
But different sized strings don’t stretch equally — the diameter (gauge) of the string makes a difference. The bigger the string, the more it will go sharp, and the more the saddle must be moved back.
The sharp-eyed among you may be wondering, then, why on acoustic guitars the B string is typically compensated farther back than the G or sometimes even D strings. Or, why on electric guitars, there often seem to be two “groups” of saddle settings (which may overlap in position); one for the plain strings and another for the wound strings.
The reason is because on wound strings, the windings don’t affect how much the string goes sharp when it is stretched — it’s the string’s core diameter that makes a difference, and on acoustic guitars, for example, the B string is larger in diameter than the core of a wound G string. On electric guitars, a plain G string will have a larger diameter than the wound D or even A strings in some cases.