Hi Victor
First, the fret placement is essentially designed to give a 
12TET    scale.  Depending on the quality of the instrument, and 
the technician who set it up, this may or may not produce a true 
octave at the twelfth fret of each string.  My experience is 
that this is only true for the most expensive instruments, and 
not all of them.
If a guitar is electric, it is likely to have a bridge with 
adjustable saddles.  This makes it possible to adjust the string 
length to produce the aforementioned true octaves.  However 
unless the fret heights are carefully set to the correct height 
above the fingerboard, and correctly placed to assure the 
correct length from the point of vibration to the bridge, they 
will be off, sometimes noticeably so.  Also, the 'bow' of the 
neck is also a factor that influences how truly the guitar plays 
in tune along any given string.  Most guitars have an adjustable 
truss rod embedded in the neck to allow correction of the bow 
that occurs due to warpage, etc.
If the guitar is acoustic, and not really expensive, and has not 
been carefully set up by a really competent technician, it 
probably won't play in tune.  And if is does, it will need 
occasional work to make sure it continues to stay in tune.
In short, the discrepancies you noted are unlikely to be a big 
factor..since the guitar won't be in tune anyway.
That said, I have found the following procedure helpful in 
tuning my very much NOT expensive guitars.
1) I tune my A-String (fifth) to an accurate source ( or to a 
source that I'll be plating with that cannot itself be tuned)
2) Using the 'Mel Bay' method most commonly found in instruction 
books, I tune the other strings relative to the A.
3) By playing harmonics at the fifth or seventh frets, I can 
check various pitches between the various strings, either by 
tuning as fifth intervals or as octaves.  If I find a 
discrepancy I choose the pitch indicated by the harmonics (due 
to the suspected inaccuracy of the fret placements).
4) I play several minor chords that incorporate open strings.  I 
seem to be able to hear discrepancies more easily using minor 
chords...one of my buddies prefers major chords..and it 
apparently is not due to our respective instruments, as we each 
tune the others instrument on occasion.
5) It invariably occurs that some chords sound more in tune than 
others...so Ill end up tuning for the key I'll be playing in if 
the effect is too jarring.
One final note..the nature of the instrument is such that it 
simply will not stay well in tune for very long..especially if 
you like the nice bright tones of new strings, which tend to 
stretch.  Most guitarists learn how to compensate to some degree 
by using string bends or vibrato to mask the sour notes.
Hope this was informative.
Bob Foose


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