The top of the buttons is supposed to be aligned with the blue line. Increasing their height doesnt do anything and when I copy+paste them into another skin it looks the way it's supposed to.
In case that's the problem Fatal3ty mentioned, you may have no Version line in your skin.ini - if you don't have one, it's adjusted to 1 by default. so if you don't have one: open your skin.ini and use a line for Version: 2.5 under the [General] part.