I'm also having issues with the category pages losing theme customizaton. I haven't been able to figure out how to fix the issue. Here's a screen capture:
The URL is MySoCalBackyard.com/burbank (or any other categories on the site).
The theme I'm using is "Dante" - http://www.mojo-themes.com/item/dante-responsive-wordpress-theme/
Any help would be greatly appreciated. :)