I am running wordpress 3.0.1 and atahualpa 3.5.3
I recently upgraded from an older version of wordpress and atahualpa where most everything was working.
I then upgraded to the latest wordpress for a security fix and it had some compatability issues with the older atahualpa. So I upgraded to 3.5.3. Since I use firefox most of the time I didn't notice any issues after upgrading. A week or so later a member was having issues viewing the site. I finally figured out that IE was only displaying the menus and not the center body of the site. The left menu is where it is supposed to be but the right menu is displaying where the normal content should be. In firefox or chrome it works fine. I have applied the two bug fixes you have posted and they fixed a minor drop down menu issue but I have no clue what is happening with IE and displaying wordpress content.
you can see the site at http://www.downeasteryachts.com
If you can help me I would appreciate it and wouldn't mind kicking a few dollars donation either.