a few people already mentioned it, but i'd guess that microphone position is the biggest culprit here....don't point your mics straight at the soundhole, and add a high-pass filter
yeah I learned that here, to move the mic to the fingerboard area..
i guess a lot of us HR heads, just assume early on to stick the mic at the soundholes?
i definitely know the sound your talking about the "boomy-muck flob noise" of the acoustic guitar playback. a totally different sound than what your ears hear.