If the guitar doesn’t normally have tuning problems then it could be old strings. When they get old they can sometimes seem almost impossible to tune properly.
If you are going only by what the tuner is telling you but it still sounds out of tune – to some extent this can be normal. The guitar cannot be tuned perfectly along the whole neck, it’s not possible. Guitar tuning is a bit of a compromise and small imperfections are to be expected. If it sounds really bad then something is wrong, possibly the intonation or a warped neck perhaps.
If you find a string is getting muted when it’s in tune then this could be the bridge or nut needs adjusting / fixing, or a neck or fret problem. You can also get this problem if you change string gauge, the guitar might need some adjustment. This happens because different string tension will slightly bend the neck and can force a fret to touch a string.
If it’s nothing obvious that you can see causing it then it might be best left to a guitar tech.
I’m not a guitar tech so I can only make a few guesses.
Can you describe what you mean by flat or muted as they are two very different things. Flat would refer to tuning, muted would refer to the sound being cut off and not ringing.
Does this happen when the strings are all played open or only when they are fretted and if so, is it across the whole neck or only in certain places.
Have you tried changing the string or using different strings. Maybe there is a problem with the E string. Also, are the strings the recommended gauge for the guitar.
What kind of warm strings? If these are silk / steel then might be worth checking if they have a particularly low tension.
Like I said, I’m not a tech so I’m just thinking up ideas.
Thank you for the reply.
This is really weird, because I bought a Taylor GS mini. I had the Tech. put warm strings on the $800 guitar and to check the action and the truss rod. Overall check to have the guitar to be the best it could be. The Low E string-Shows to be tuned but it sounds flat or muted and all the other strings sound ok. I am not sure about keeping the guitar, with a bad sounding string. I just don’t understand how this can happen. Do you have any other thoughts about this?