The added weight of the boats is what makes then more stable. Having a heavy boat means that the weight of the passengers is a lower percentage of the total weight. What that gives you is less difference in boat behavior from empty to full. I don't have the facts about the two rides But I would guess that the water is deeper in the maelstrom, allowing boats with a larger draft i.e heaver. It sounds like the old POTC boats had issues with hanging up when over loaded, probably due to the heavier design. One would think the idea would then be to lighten the boats thus the draft, but when you do that, the difference between a heavily loaded boat and a lightly loaded boat can be drastically different. This can lead to listing side to side, as well as the attitude shift forward to aft. (Because the passengers are a higher percentage of the total weight, they make a bigger difference.) So slight difference in passenger weight and balance cause radical changes in how the boat strikes the water at the bottom the waterfall, and how it goes through the water.
If this is the issue, the fix is not an easy one. Heavier boats would probably fix the problem, but they sink into the water too far. so to make up for the increased weight you would have to make the boat physically larger to displace more water with the same draft, but the track is a fixed width so you cant go in that direction. the only direction to go is to make them longer, That is a problem because the corners are tight and longer boats would not make it around the corners, and the space between the boats on the loading platform would probably be an issue as well. The only other fix is to make the boats heavier, and load them less people, but then the ride capacity goes down.
The only for sure fix is to put wheels on the boat so the weight is born by the wheels instead of the water. but then it isn't a boat ride is it? it is an water filled omnimover (OK OK i know the difference, just making my point by being absurd) I would rather have to go in my swim suit than make it not a boat ride.