Every input of your TV (HDMI, HDMI2, Component1, Component2, RGB, etc) will have a separate control for AutoMotion.
So... its possible that AutoMotion is turned off, or at a less noticable setting on some of these inputs... So adjust them to your liking under the MENU screen, for each input.
I am curious as to how the source affects the look of the 120Hz Auto Motion Plus.
For example: When I am watching Blu-Ray movies on my PS3 via HDMI, I can see that cool, smooth "video" like look which I know some don't like but I really just love. However, I don't notice it as much when I am watching, say DVDs of "Frasier". However, when I first got my TV (Samsung LNT4071F I beleive), I remember watching Airplane! on it on the Xbox and seeing it smoothed completely! It was really neat!
I also do not notice it as much through my Apple TV (720p, Component video), my comcast cable box (720p, HDMI), my Xbox 360 (1080p, Component video), or my Nintendo Wii (480p, composite).
So is there some trick that I am missing to get it all smoothed like that, or does the source material (resolution and refresh)affect how the Auto Motion Plus works?