I agree with nell's first comment. Your rudder isn't stalling, it's coming free out of the top of the wave. The only way you could be stalling the rudder is if you put in full deflection on the pedal very quickly, like jamming the rudder full over at speed. This isn't very likely. When your rudder breaks free, the boat wants to broach because the crest of the wave is moving the back of the ski forwards while the trough is pulling the front of the ski back, thus yanking the hull out of line.
Short, steep waves are the cause. That's why Epic moved the rudder forward a couple of inches on the V10L and why the straight elliptical rudder is better than a swept rudder - these serve to keep the rudder blade buried.
One thing I've done when I can feel this happening is to tilt the boat away from the wave - like you're leaning towards the downhill face of the wave. This seems to angle the rudder blade back into the wave a little. Sometimes it saves a run, sometimes it don't. The only other way to deal with it is to pull hard on the up-wave side and try to torque the hull back down the face with your body. Sometimes it works, sometimes it don't.