OK, the subpage_style template shows a number of changes by Daniel in March 2009, and a single one by Caesar Schinas on 3 May 2009. Caesar's change is noted as "removed side margin to align subboxes with other boxes" and something about not being sure he was removing the right thing. Could someone (Daniel?) look over his 1 digit change to see if it is the likely bug source? There have been subsequent changes in Aug or Sept also.
Did your conversion to Chris' old version help? I just checked the history and do not think Caesar's edit is the culprit. However, to be sure, I undid it. Please check whether this makes a difference. However, I have already stated what I think the reason is, and if you are done checking Caesar's edit, please let me know, and I will undo the edit that I think is the culprit, as explained at
http://forum.citizendium.org/index.php/topic,2939.msg24985.html#msg24985 .