Upgrade 5.4.05 to 5.4.11 page edit broken

Permalink
Just upgraded a site from 5.4.05 to 5.4.11. In edit mode, when i attempt to edit a block, instead of opening the modal window, I get a new page without any styling.

Looking at my page source, I see two issues: multiple copies of jquery.ui.js loading, and the site is now pulling everything from the 'updates' directory.

I already flushed the site cache. Shouldn't the upgrade actually copy (& overwrite) the files into the root concrete folder, rather than refer to the updates folder?

I know how to track down & remove extra copies of jquery & other .js & .css files if they're included in an add-on.

How can I fix the folder issue, and actually merge the update files into the installation?

invision