A good room is not just important for the tracking, it's also impoortant for the mixing. If your mixing room is playing games with the bass response (a common occurance in project studio situations), this can effect what you're hearing from your monitors when you mix and when you play back your mixes in that room. Affecting what you hear on the low end can certainly have begative effects on how your resulting mix sounds when played back elsewhere.
That said, though, definitely try the tricks with bandpass as recommended above. Also, on the acoustic, mic selection and placement can make a huge difference (e.g. if you're getting too much from the sound hole at the wrong angle, that can add some mud to the track).
If after those adjustments in the recording and mixing techniques still don't solve the problem, then it's definitelytime to look into some mix room tuning.
G.