One of my planes has waaay too large of an engine on it. Everything is balanced, but there just isn't enough mass in the model to dampen the engine vibration. At idle the plane looks like it's trying to shake itself apart. Once the throttle is advanced a little it calms down. I've put the plane in several terminal velocity power dives and there is no flutter.

My point being that what you're experiencing may be normal, but you should make sure everything is fastened securely and anything attached to the engine crankshaft is balanced.