I recently found that the 'Active Site Theme' didn't mean what I thought it did. It's not a site setting or a flag in the PageThemes table. When you click to activate a theme, what you're really doing is assigning that theme's ptID to all pages except page type defaults (templates) and core single pages. You can then assign individual themes to specific pages.

But how does C5 know which theme to display as the 'Active Site Theme' on the the themes page so it can disable that button? Well, believe it or not, the 'Active Site Theme' is simply the theme currently assigned to the home page!

If you set the theme for your site to Plain Yogurt, then edit your home page to set its theme to 'Dark Chocolate', 'Dark Chocolate' becomes the active theme for the site - even though the home page is the only page that is using that theme.

Edit: The page type defaults will display with the 'Active Site Theme', so to continue with the above example, after changing the home page theme to 'Dark Chocolate' if you go to Dashboard > Pages and Themes and click Defaults for any page type, you will see it rendered with the 'Dark Chocolate' theme.