I also feel like this is affecting zooming as well. When you scroll it is supposed to zoom in on your mouse, but in our situation it seems to be zooming in somewhere other than the mouse location.
The map is inside of a window that was made with JQuery UI that is draggable and resizable. If I resize the window to the full size of the browser window, then things seem to line up. Has anyone else run into this problem and have a fix for this?