Also, press CTRL-J in-game to disable the controller. If you have a game controller (gamepad or joystick) connected to your system, please try disabling/disconnecting it from your system before entering the game to see if this helps. When you are in the raft moving through the water, please avoid pressing the shift key while navigating the raft.
After installing the 1.1 update, please load-up a saved game before this area (preferably before boarding the raft) and then advance again through the swamp and back up to this point of the game. We have seen this problem before and apologize for the inconvenience.