Did you delete the save folder prior to the re-install? If you didn't, the install may well see that the folder is there, and then leave it. You go and delete it afterwards, and the game will re-create it, but with the bad data still.
But something is strange... of course, "strange" surrounds us everyday in our lives...
I would think that if it's a DirectX thing, you would have more symptoms than just a few boats. Are you using an original disk (or good copy) for the install, or do you have a downloaded version? If a download, and you can, I'd try a new download of the install (archive it after the download).