Better WP Security and Thesis Theme

In a nutshell, I installed the Thesis Theme and the Better WP Security plugin, changed a few settings and files and now I can’t access the Skin Editor in Thesis. Below are the details.

First, I have WordPress, and subsequently the Thesis theme, installed in a subdirectory.

Second, when I used to access the Skin Editor in the Thesis theme, it used to open 2 tabs: one tab was the Skin Editor and the other was the website itself that I was editing. No problem here.

Then I did the following, not necessarily in the order written:
I installed Better WP Security and ramped up the security of my website with many of the suggestions offered.
I enabled the permalinks and updated the .htaccess file.
The “index.php” file was duplicated, moved to the root level, and edited to redirect to the index.php file in the /wp/ folder.
I have a copy of the .htaccess file in the root directory and in the /wp/ folder.

Here’s the issue: At some point, one or another of these changes caused the Thesis Theme Skin Editor to be inaccessible. Now when I go to open the Skin Editor, there seems to be some kind of redirect and only one tab opens instead of two. The tab that opens shows only my website and not the Skin Editor. When I hover over the “Skin Editor” link, I see one URL which indicates a location that digs down into the subdirectory and the wp-admin folder. When I click on this link, it redirects to a different URL (a root directory location) and shows only my website. I can access all other parts of the the Thesis Theme: Head Editor, Skins and Boxes. I even played with the Head Editor and put in a favicon and it worked fine.

Can anyone figure out what file, files, setting, or settings need to be temporarily changed or reset so I can access the Skin Editor again?