Maybe something went wrong when these changes were made:
https://meta.discourse.org/t/users-not-notified-by-email-of-private-messages/15894/11?u=wesochuck
or maybe something to do with the wording changes that happened with the “Active on site” preference (I think this was the post that initiated that change):
https://meta.discourse.org/t/convince-me-to-transition-over-from-google-groups/31221/13?u=wesochuck
I also impersonated the user just to make sure that they hadn’t Muted a particular topic (they had not).