Hi,
I would use y custom solution using the new UI system and an image without sprite that covers the full screen, then you won't have flashes likely.
also, check your code maybe you stop fading one frame too soon or don't wait for the scene to be really loaded. If you use LoadLevel you don't when the level is really loaded ( especially if big), so have an fsm in the next level that sends a global event "I AM LOADED" or something so that your fading system knows exactly when to act.
Bye,
Jean