I had a temperamental Suzuki RF600 many moons ago that didn't like getting wet. Turns out it was due to the coils being bolted onto the inside of the frame and the water ran between the tank and the frame straight onto the coils.

It would run on 3 cylinders when this happened and I had to keep it in a low gear at a constant throttle until it cleared itself.

Is the bike kept outside? Been stored for any length of time? Using a different petrol station? Changed spark plug recently? Is there a strong smell of petrol when it's not running right?