Do you have an open air filter element and an exhaust leak? If so it could be the carbon monoxide that is choking it.
When I first got my jet boat, the water log headers leaked exhaust a bit, I didn't think anything about it but after about 15-20 min out on the water the thing would start running bad and have no power. Id open the engine cover and it would run normal. Then after another 15 min, it would do it again. After a couple beers at the camp fire that night, it dawned on me that the thing was choking itself out from the carbon monoxide. I wedged a couple small 2x4's to keep the engine compartment slightly open. That gave the engine enough fresh air that it ran great the rest of that trip. Then I fixed the exhaust leak when I got home.