Hey, so I have a Taylor guitar, and I'm having some trouble with it. I never used to have issues, but all of the sudden I took it out of its case (that does have a humidifier btw) and the 12 and 1st fret are in tune, but the 3 to the 5th-ish... are noticibly not. The neck looks straight. I have a truss rod wrench, should I tried tweaking it a little bit and seeing if that helps? I hopefully don't have to pay $60 for someone to set it up for me.... Thanks!
On a good quality guitar like a Taylor, if the intonation is OK on 1st and 12th frets it should be OK on the 3rd to 5th frets also.

HST it is a fact that an acoustic guitar is not a precisely intonated instrument and even with normal playing there will be some notes that are out.

Try reducing finger pressure when you fret at the offending frets? Does that help? Also it might be an idea to change strings.
Don't start tweaking until you check the neck relief first. You'll also need a set of feeler gages preferably(or at least a business card) and a capo to check the neck relief. http://thbecker.net/guitar_playing/guitars_and_setup/setup_page_01.html

Improper neck relief can cause buzzing but I don't know if it would cause a guitar to be out of tune on some frets but it may be possible. I'm no expert by any means.
Last edited by rohash at Oct 20, 2014,
I would suspect the strings. Nothing should change the intonation of the guitar itself.... That's strictly a function of string length and fret placement.... Which should be pretty much spot on with a Taylor.

So something else is likely going on. Replace the strings. Then, using an electronic tuner, make sure your intonation is correct by playing the fretted note at the 12th fret and the harmonic at the 12th fret. They should be the same.
If not, I'd check with Taylor for your local authorized repair center.
Let us know the cause when you get it figured it out. It might help one of us in the future.
Main two things that cause intonation problems with acoustics:

Dead strings

Fretting too hard.
Hmmm...I wonder what this button does...