What is exactly wrong with the boats?
Square peg, meet round hole.
The new fleet of boats are the same as what was created as replacements for and being used on the original attraction in Anaheim. Even in Anaheim, they aren't a perfect replacement as the new boats aren't as buoyant as the old fiberglass ones, so they sit lower in the water and the bow of the boat is more steep.
One Disney brainchild thought it would be a good idea to save costs in Orlando to use the boats engineered for Anaheim, so they were hastily put into service at MK.
At the MK, the main issue is the drop. At DLR, the entrance to the drops and runoff from them aren't as steep as MK. The boats come down into the water, the bow plows into it, the boat decelerates much more rapidly as the water tries to displace, so it creates a wave, the wave washes over the bow and dumps a bunch of water into the boat, the boat then sits even deeper into the trough and adds more weight, compounding the problem the next time it cycles through.
Oh, and the new boats are structurally not as sound as the old ones... which when you combine with the extra weight from the splash... you end up with the need to rework the attraction. Especially when the chassis is being flexed as it enters and exits the drop and even on the lift at the end.
At a minimum, the drop and runoff will need to be reworked to keep using the current fleet of boats.