With the lastest version I'm only getting emaisl to work when a user clicks on the "Email me when this thread has replies" or  "Email me when this Forum has a new thread."

Uers who subscribe to notifications from a forum, a notification forum type, clicking on the notification checkbox on a post/reply, these do not send out emails.

Any ideas why some ways work well others don't? I'm using scheduled emailing.

Along the same lines...  When I click the notification checkbox at the bottom of the page (on the DNN forums - here), the page reloads, but the checkbox is never checked.  :(  I never receive notifications for a handful of my posts.

Agreed.  At the time of writing the initial post here, I had some leftover e-mails from before the module upgrade, so I thought that at least some of the e-mails were getting through.  As you verified, this simply is not the case.