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.
Lee Answered question June 3, 2019