I have a 3 string CBG tuned to open G. Digital tuner indicates it is in tune and intonated.  However, when I bar the 5th fret the tuner registers a D cord instead of a C chord. Anyone know how to correct this? Strains are Southbound .042W, .030W and .022w.

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If it’s a floating bridge instrument the first thing I would check is if the bridge is located correctly. Make sure it’s twice the distance from the nut as the 12th fret is.

thats a whole hell of a lot outto get a d instead of a c. try the individual notes tuners dont do chords well. check for C,G,C at the 5th fret. assuming the open strings are G,D,G. check that first. 

Fretted or fretless? Your nut may be too high? If not confirm that your scale length is correct? If your using a bolt for a nut, then measure from the middle of the bolt where the strings touch to the middle of the bridge where they also touch? FYI a guitar tuner can register that the strings are in tune when played open, but does not necessarily mean the intonation is correct? Without seeing the guitar, those are the 2 things I would check, next time try to give more info or pics, it’s hard to diagnose if you can’t see what’s wrong? Good luck on this

Going back to basics usually identifies issues. My apologies if these are things you've already done.
1. Measure from the nut to the 12th fret. This should be exactly 1/2 your guitar's scale length.
2. Measure from the nut to the bridge. It should be exactly twice the distance from the nut to the 12th.
3. If those are both okay, recalculate how far the 5th fret should be from the nut and check to ensure that it is correct.
4. If #1~3 are all correct, check the tuning of individual strings. Is it in tune open and in tune at the 12th? If so, check it at the 5th. If the 5th fret is in the correct place, then it should be the note you expect.

It sounds like a lot of measuring, but won't take long and then you will be sure your set up is correct.

Let us know what you find.

Individual notes read D, G, D.

Nut may be too high. Using 1/4” threaded bolt on fretted neck. String height is 3/32 at 1st fret and a hair over 1/8” at 12th fret. (1st string).

Tuner indicates strings are in tune when open and fretted at 12th fret.
All basic measurements are correct. Made a discovery. Digital tuner was set to G because I am using open G strings. When I changed the tuner setting to C (chromatic) everything is in tune and I get a C chord at the 5th fret. How should the tuner be set? Totally confused.

G will always be G, no matter how it’s set, but if you’re confused about how to use your tuner, then go back to the default chromatic setting, this covers c d e f g a b c respectively & is less confusing? Look for a video that shows how your tuner works, I’m sure there’s one on the internet (I know people don’t like to read manuals) Also, if you get G played open, what do get on the 1st fret? If it’s sharp, then the nut is too high? 

Glad you got it sorted.

Now, how does it sound?

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