Hard to know what you mean when you say "muffled", but maybe, since you say it's often with the smaller models, it has to do with the strings themselves and inharmonicity. In a smaller instrument, the bass strings have to be thicker to compensate for the lack of length, and the strings can also overlap each other more (strings aren't parallel, as they were once upon a time in pianos). Some say that these things can create a more muddied or maybe "muffled" sound.
Or do you mean something more like volume?
I'd be curious if you notice any patterns if you look inside the ones you say sound "muffled" vs. the ones that sound better to you.
JH