Tuning issues with recording an arpeggio?

[Sssssnrub]

Hey everybody, first time poster here.

I have come across a bit of an issue with recording a composition I've written. This issue seems persistent across all my different guitars, and has to do with two specific voicings featuring open strings.

The voicings are for an Em(add9): xx2002 and a Fsus2(add#11): xx3003.

The open strings sound out of tune no matter how I change the tuning. I've so far tried; tuning sharp/flat by a few cents, tuning to where the chord being strummed sounds in tune with itself, tuning to where the arpeggio sounds most in tune, used several different types of tuner, and obviously tuned to as perfect to standard tuning as I can get.

Is there perhaps a specific reason that these notes are so hard to get in tune and is there anything else that I could possibly try to get this part to work? Or will I have better luck cutting my losses and just changing the part?

If I've posted this in the wrong place, I apologise, and thanks for taking anytime out of your day to read/reply.

[sgosnell]

A common cause of this is that the nut slots are too high. Almost all factory-built guitars come with high nut slots, because it's time-consuming to get them to the right depth, and going just a little too far means starting over with a new nut, or filling the slots. If the slots are too high, then fretting near the nut pulls the notes sharp, and the open strings sound flat. A good setup is essential for good intonation. If you don't have the skills to do the nut work, take the guitars to a good luthier/tech for a setup, and clearly explain what you expect.

[Mick-7]

Guitar nut and fret irregularities, like the one that sgosnell mentioned, created the market for the Plek machine service and why dealers like Sweetwater promote it for the new guitars they sell.

[strumcat]

Guitars with this problem, when tuned to exactly correct open-string pitches, will sound excruciatingly out of tune when cowboy chords are committed on them. Typically, a cowboy D-chord will have a very sharp D on the B string, and a cowboy A-chord will have a very sharp A on the G string. In a pinch, I use the following tuning method to mitigate the problem.

If you're using a tuner, make sure it's set to "real exact pitch" mode instead of "guitar compensation" mode or whatever. Otherwise, just tune the D string first, then use it as a reference to tune all of the other strings (as directed) in precise octaves, fourths, and fifths.

Tune the open D string to exact D.
Tune the open A string to exact A.
Tune both E strings at the 3rd fret to exact G.
Tune the B string at the 3rd fret to exact D.
Tune the G string at the 2nd fret to exact A.

All of the strings tuned while fretted will be a little flat when played open. All of the open-strings-plus-fretted-strings combinations played near the nut should sound more or less "flanged", but none of them should sound wildly out of tune. I'm curious to find out if this works for others, too, or if I'm just being delusional again.