I have a HBFP and had the vibration curse for some time. For me the problem was the crash gear. It apparently induced a harmonic vibration which caused the whole heli to shudder. When I took them off it smoothed out immediately. The only other times it happened acutely was when I broke one of the ring links or one of the hub pitch hinges off (the bearings for the head) causing it to vibrate until I replaced it. It did, incidentally, still fly and I therefore didn't notice it until I carefully inspected the head.

Also see this for excellent methodical advice on eliminating vibrations:

http://cory.butzon.com/blog/?id=177