Not sure how helpful this is, but...
I had an Eastman guitar in for some setup work. I noticed that if I played the bass E string at the 12th fret - an E note - it had a very, very short sustain, a "thud", and almost no harmonic/overtone component to the note. If I played the same pitch on the A string, 7th fret, it had considerably more duration, less "thud" and more harmonic component. If I played the same pitch on the D string, second fret, it had far more sustain, far more harmonic content.
I found it sufficiently interesting that I recorded these three notes in Audacity to more clearly examine the response I was hearing.
I didn't find a cause and effect and eventually chalked it up to a "mediocre instrument". Not very insightful, but I found it interesting as it is rare to find an instrument with that striking a difference in response when playing the same pitch on different strings.
I've also had instruments that had a "thud" like response on notes fretted over the top - the fingerboard extension. I theorized that those notes were physically unsupported by the interior structure and the string's energy just dissipated. I did a few tests with soundpost-like pieces to attempt to bolster those specific frets, but didn't conclude anything specific, as in cause and effect. One of the places where I've seen this most is in fingerboards that are fully unsupported that extend into the soundhole, for extra frets for the top one or two strings.
In short, it probably has little to do with the situation you are encountering, but thought I'd throw it out there in case it stimulated some thoughts that might be relevant.
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