I've just verified that there is a bug somewhere relating to saving the options related to the settings tab.
Try this to verify:
1 - Bring up a view of the options table in your mysql interface of choice.
2 - search for this option_name: "ny_subscribe_theme_css"
3 - Keep that window open and watch the option_value.
4 - Now bring up the settings tab under Navayan Subscribe
5 - Uncheck the "Use active theme CSS for email templates" box and save settings.
6 - Refresh your view in your mysql interface and see that the option_value is now 0.
7 - Now click any other link in the wordpress admin panel (left sidebar) - "Posts", for example.
8 - Now click back to the Navayan Subscribe link under Tools.
9 - Look over in your mysql interface and refresh your query and notice that the option_value is now 1 - WITHOUT YOU HAVING CHANGED THE CHECKBOX.
10 - Now click on the settings tab and scroll down and notice that the "Use active theme CSS for email templates" checkbox is now checked, even though you did not check it again.