The fact that you're also getting window rattling sub bass in passive mode suggests, to me at least, that the pickups are the problem here. I'm not up on Yamaha models but is this the same model, or at least the same pickups as in the white Yam 5 sting of yours that I heard in action a couple of years ago? That bass had a lot going on it the lows, too much for my liking, and it sounds like it could be the same thing going on here. If that's the case I'd be inclined to lower the pickups into the body away from the strings to let the bass breathe more, or if that doesn't cure it, look to replace them with something less subby. You can, of course, use a patch on the Zoom to compensate but that's more a case of putting a plaster over it rather than addressing the actual cause of the problem in the first place.