In order to keep from re-posting an issue in a different area, please take a peak at the "Simple Notices" plugin issue, I reported here: http://wordpress.org/support/topic/plugin-simple-notices-conflict-with-twenty-eleven-13-css
Assume a clean, self-hosted install of WordPress, with no other plugins enabled, and no configuration changes made to WordPress...
What is the significance of the z-index of #branding (in the Header div) being set to 9999 when the 2011 Theme is active?
and...
Why is the z-index only affecting the border-top and not all the remaining elements contained in the Header div?
