I don't think thats a flat spot mate. I used to restore old bikes and you'd get a flat spot on acceration, normally caused by a worn throttle slide on the carb. Now since your car doesn't have a carb and you say its fine on accelaration I don't think its a flat spot.
I've just tried what you do with my BRM, as they're essentially the same engine, and I can feel a couple of small of jerks. I reckon Its just the clutch being freed from the torque caused accelation. The clutch should have some springs built into it to absorb this force and its these that you can feel acting.