I think I understand your problem. My first suggestion is to instead of positioning the objects yourself, look at the values of the object in the properties bar and make sure the Y values of both of them are the same. This will not work if their image points are in different places or if they are different widths, but just do a little math to make sure they are precisely lined up pixel to pixel.
To prevent this from happening in the future enable grid lines and grid snapping in the layout options.