This is just a guess, but it could be the secondary throttle control valves aren't working right.
The throttle bodies have two butterfly valves in them. The lower ones are controlled by your throttle, and the upper ones are controlled by the ECM. So if you snap it open too quickly the computer won't let the upper ones open as fast so the bike won't fall on it's face. It works kind of like vacuum secondaries on carburetors, but the ECM controls it instead of engine vacuum. If the secondary throttle valves get out of adjustment I could see it causing your problems. For instance, if they don't open the injectors could still inject fuel but the secondary throttle valves wouldn't open to admit air, so it would be rich. There is a check and adjustment procedure for them posted just a day or so ago, but I'm not sure if that would help or why they would get off. If they aren't working at all it sets the FI light.