There is no way a 28ft triton should dive under water. It may be possible if you were running fast and immediately stopped boat as it got hit by a big wave, otherwise, it shouldn't happen. You said that dad was slowing down, so the above scenario couldn't happen.
We boat on Lake Lanier, 38,000 acres and we have a lot of big boats on it. We have hit waves over 3ft and never taken on a drop of water, I don't slow down for waves.
Something is just not right under your boat.