I currently have WP 3.04 and Atahualpa 3.6 (about to update) but have had the same problem with previous Atahualpa theme.
I am trying to format my comment box and comments at a padding-right: 50px.
I have the border between single comments at default and my comment form style includes margin: 25px 50px 0 0;
My problem is that the color shading, text, and border are not with the padding. Please see the attached image.