I agree with what's being said about the Barts. The Sei I had for a while was Barted, and they were pretty crap to be honest: like yours, the bass sounded wonderfully lively when played acoustically, and the piezo bridge sound suggested that the bass should have sounded stunning, but when the Barts were dialled in it just went [i]bleh[/i]. If I'd kept the Sei, the Barts would have quickly gone. So yes, I reckon it's yer pups.
Might it be possible to test the theory out by temporarily fitting something else -- anything really, even if it doesn't fill the cavity properly -- and seeing what happens to the sound? If it changes dramatically, you'll know. Martin P's definitely the guy to go to.