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.

Could you supply a link to your site please?

http://www.recipesandrunning.com

I appreciate your help.

You have to have 50px right padding in ATO>Style & edit Center Column and then tweak the comment form style. For example... After adding the 50px right padding on the Center Column you will want to have no right margin for the Comment Form Style

Center column style now is set at - padding: 10px 50px 15px 0;

Also, Style the Navigation MIDDLE Box and Style the Navigation BOTTOM Box
have margin: 10px 50px 20px 0;

I removed my changes to Comment Form Style to default of margin: 25px 0;

I am still running across the same problem though. It seems like the center column style padding is not applying to the comment area.

It looks like you have vestiges of the original default style in ATO>Add HTML/CSS Inserts>CSS Inserts. Try taking our or commenting out the following.

/* removing the padding here and putting them on the sidebars instead. That way the middle column aligns nicely with the header when there are no sidebars */
td#middle {
padding: 0;
}

Perfect! Thank you so much for all your help.