#1
I was wondering if I'm having a real intonation problem or if it's just a case of the guitar exhibiting "natural" intonation inaccuracies that I've heard about.

I was testing my intonation on the low E string and noticed that my 5-7 frets were pretty sharp, from 6 up to 10 cents high. All the other frets are in tune, some with intonation problems but under 5 cents only. Also the E on the 12th fret tunes perfectly as well.

Thanks to all for your help!
#2
Is it only the fat E or also the other strings in the same region? If that is so, check the neck curvature. It might be a little too much bent forward. Tightening the truss rod will solve this problem.
If the other strings are fine, or the neck curvature proves to be inside established tolerances, you can look for unevenly worn down frets. If these check out fine also, it might just be a set of strings that happens to be less than perfect.
About the 'realness' of these intonation problems I'd say; if it only shows up in precise measurements but doesn't annoy you or your band members when playing, they aren't there. If you can't hear it, your audience won't notice either.
#3
Because the guitar is considered an "equal tempered" instrument, you will never be able to acheive perfect intonation from it. The physics of it make it impossible, so a balance has been struck over the years to make the guitar at least sound close. An extreme fix is the "True Temperament" neck. The frets themselves are compensated to allow precise tuning and playing. It looks like the luthier who built it was seriously drunk, but I do understand the theory behind it. Here's the link if you wish to read more about it.
Btw, if the only string that's off seems to be the low E, then perhaps you may need to compensate your bridge saddle. Usually tho, these innaccuracies appear up around the 1-3 frets, not 5-7, although they certainly can show up there as well.

http://www.truetemperament.com/main.php
#4
Quote by LeftyDave

Btw, if the only string that's off seems to be the low E, then perhaps you may need to compensate your bridge saddle. Usually tho, these innaccuracies appear up around the 1-3 frets, not 5-7, although they certainly can show up there as well.



You're right Lefty. Indeed it is true that guitarist have to live with one intonation problem or another. Guitars are no instruments for those challenged by perfect pitch hearing disabilities. Neither is any other musical instrument, for that matter.
However, I must correct you on the above quoted statement. Intonation problems round the lowest frets must be corrected by changing the string heigth at the nut. It is deviations around the upper frets that must be corrected at the bridge saddle, either by changing the string heigth or the string length.