Did you switch over to a two light system in the rear, where you brake lights and rear turn signals are in the same trailer light? If so what is happening is when you step on the brakes the turn signals are turned off and the brake lights come on. This lowers the resistance and your blinkers speed up, thinking that your rear turn signal light bulb has gone out.
Mine do the same thing. The way to fix it is get get a powered trailer light box instead of the cheap one you are using. This way it will be smart enough to keep the turn signal blinking even if your brakes are on.
Not sure about the hazards though. I'm not sure I even have the switch any more...