Same thing happened to me after an engine rebuild. Yes, you have an air leak. If it happens again, just pull kill lanyard AND squeze full open on throttle. Engine will stall.
Had the same problem on a 2000 GP 800. After PM, new plugs, spray lubricant on all the exposed carb and valve linkage, cylinder lube, greased the main drive bearing and replacing the fuel filter I pulled the Carb cover and Flash suppressor so the Carbs were completely open. Be very careful if you are not putting the flash suppressor screen over the Carbs and starting the engine (not recommended), put the screen on before you start it (each time), its a good way to start the ski on fire. I loaded the carbs up with Carb cleaner three or four times a day for three days, went through an entire can. Started the ski about every other treatment and was constantly working the throttle while spraying the carb cleaner into the carbs. After 6 days, two tanks of fuel and three trips to the lake the ski is running like new.Thanks, we will start there.
If anyone has anymore ideas please.. Post.