I haven't had time to read all of the replies, but I too had a bad experience having just returned home from a trip. I rode POTC the morning of October 25. I stepped into the boat on the 4th row, right hand side and would estimate approximately 1-1/2" - 2" of water standing in the bottom of the boat. So, I made a point to keep my feet on my tip-toes throughout the ride.
As we departed the loading area, the boat seemed to struggle and scrape on the bottom, right hand side of the boat. We continued throuout the attraction very very slowly. I felt the attraction was moving along much more slowly than it should... enough that it became tiresome.
Halfway through the attraction, I was having to pull my body to the left by use of the seat handles in from of me to keep from leaning out of the right side of the boat. All of the passengers in the boat were leaning to the left to keep the right side of the boat out of the water. There were times when a small wave would come over the right side of the boat soaking me. I left the attraction with wet shoes, wet shorts, and a partially wet shirt.
I left the boat slowly and was the last to depart so that I might intentionally look to see how much water accumulated in the boat. It had significantly increased to somewhere between 2-1/2" - 3" by my approximation.
C'mon Disney. We need this issue fixed and resolved promptly. A member of my party politely addressed this issue with a cast member/guest services.