Water in the hull seems to have been the problem. I wasn't running the bilge pump often enough and as a result, the engine was having problems and acceleration was very sluggish. We were having these problems after about an hour and a half of riding, twice today. Thought it might be the "knock protection" mode and unplugged the battery unsucessfully.
Brought the boat into the dealership and to my embarrassment there was way too much water in the engine compartment. For the rest of the day, I ran the bilge to remove excess water at least every half hour on the water and didn't have any problems! (another 6 hours of tubing, skiing and wakeboarding- we were hosting a fraternity rush function this weekend and had 30-40 guys staying at the house).
-Nate