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I have specifically opted in to being notified of replies to a number of threads/posts, using the opt-in check boxes under the editor when posting.  I've also used the 'Watch thread' link at the top of threads a couple times, but I haven't recieved any email notifications, ever. It's not a case of checking my junk mail; I do check that frequently, and nothing is there.  Plus, I've added XF to my whitelist anyway.

A couple things I've noticed regarding this issue:

In my account settings, under 'Watched Threads', when I click 'Show all watched threads', I see check boxes labeled 'Email'.  Since these boxes appear to be used for the options in the drop-down below the list, I'm assuming the threads that have already been selected for notifications should be auto-ticked?  I could be wrong about that part, but whatever the case, I'm not getting the emails.