I recently posted a post about the sites that has check boxes for both “Subscribe to comments†AND “Notify me of followup comments via e-mailâ€. Isn't that the same thing? Or have I missed something here? Post: http://www.infektia.net/errors-or-what/
I don't know about the site you used. Here at DP you can subscribe to a thread and elect to receive notification of new posts via email if you want. This is a very handy feature to learn how to use when you want to see the follow-up posts but don't have anything of value to contribute to the thread. If you don't select email notification they appear in your control panel under subscribed threads the next time you login. This is a common feature of the VB scripts. I think is an optional setting controlled by site owner.
It is the same thing. Most probably sites having 2 checkboxes are those who install Subscribe to Comments plugin + Brian's threaded comments. brian's plugin detects subscribe plugin and put its own checkbox whereas people also implement in their theme subscribe checkboxes and end up with 2. Check any one of them and you will be subscribed to comments.