Comment 4 for bug 1852255

The alignment is done relative to the pad that you right-click on to run the tool. That means that the other pads will be moved to align with it. In your example, since you click on pad 9, pad 7 moves to be aligned with pad 9 (either the top of pad 9 or the bottom of it). If you want to align with the top of pad 7, click on pad 7 and run the align to top tool.