This problem occurs when in the given content a javascript is executed to fly out a javascript select menue. Lets say the div has a height of 200px the content with closed flyout has 300px, so a scrollbar is visible. now when the flyout gets activated the div still only has 300px worth of height even if the flyout contains a height of 500px. (This results in the overhead of flyout acting as if it was overflow:hidden past the 300px content. This problem did not occur with the gecko render engine, nor with the trident render engine so i assume it's a matter of webkit having a little bug there.
Care to attach a small misbehaving page that shows this problem since it seems that you did some testing against other browsers?