Yes, the ride up the back is always less smooth than up the front.
The 747 does bend, and the Yaw Damper system is designed to reduce the effects of this. There are accelerometers at either ends of the fuselage to measure the bending. This is called Structural Modal Oscillation.
Perhaps the system was partially inoperative? I think you can fly with one of the two Yaw Damper Systems inop. One system controls the upper rudder, and the other the lower rudder (The rudder is split into two) I assume the effectivity of the system is halved by doing this (at least at the extremes of control).
Rgds.
NSEU