As I commute to work, I experience the said bump often. It appears to happen if you are sitting in the back of the a/c, and not in the rows in front of the wing.
It has nothing to do with thrust reduction or flap retraction. It happens much earlier, in the rotation, when the wings start producing lift and the aircraft just leaves the ground. There is ohwever a noticable difference between flights/ rotation rates etc.
I think Johnt T. is about right, but I cannot explain the effect myself at all...
P77