Domain theme replaces current $conf variables with domain specific ones.
So when zen_theme_get_default_settings is called when getting theme settings it saves the domain specific settings into the main theme settings.
The effect of that makes the main theme have domain specific settings to the last time a domain specific form was Viewed (not submitted!) (if the theme has domain specific settings when viewing form).
How about an additional param to zen_theme_get_default_settings to indicate not to save or advice on how to do theme specific settings for zen sub themes without zen_theme_get_default_settings being called?