Was this a brand-new bike, or even a used one that has been on the showroom floor for a long time?
My bet is one of the carbs is dirty or clogged.
A quick test:
From a dead-cold bike, start it up and run it for no more than 10 seconds. Shut it off and VERY CAREFULLY touch the exhaust pipes about six inches down from where they exit the front of the engine. If one pipe is hot and the other is not, that means that the cold side is not firing properly. (Can be due to carb or fouled spark plug, or ignition system failure.)
If you have access to a laser IR thermometer (Harbor Freight sells a nice one for around $50) you can measure the pipe temperatures, they should be within 25-30 degrees of each other when hot.
Ninja Boy was BRAND NEW but had set on the showroom for an extended time, the #2 carb was gummed up and it was running on only one cylinder the second time I started it up. The dealer sent a truck, picked it up, cleaned both carbs and it was fine after that.
If it was new (or used brought from a dealer) take it back and make them fix it.
I have come to terms with the possibility of dying while riding, life has a 100% death rate. I would rather live having fun and end up dead in a motorcycle crash than never do anything fun because it's dangerous and I might get killed. No one makes it out alive anyway. - From a friend on another forum, used with his permission.