core theme settings cannot be initialized

I was having a little problem with the themesettings API; While all my theme settings default are loaded when a theme is enabled, I seem to be unable to set default settinsg for 'toggle_search', which controls the theme-search-block.

It looks like the default settings won't load for any of the settings that are part of the Drupal core settings, even though these are stored in the same variable as custom theme settings.