Having the flywheel and dampener on during balancing is best, this eliminates any problems with the two end items being out of balance themselves, also yes the viscous fan could be an issue too. Then again, it could be something different altogether like a worn universal joint? usually its the rear one on the tail shaft that goes first. Easiest way to check them is have the car in neutral with chocks under the wheels(engine off!) and get under the car and turn that tail shaft hard by hand, if you see any movement in the ends replace the uni.
