Yes, they show up as "New" / unread in the thread but that first alert never comes. All usergroups set to have Maximum tag alerts per message set to unlimited. alert preferences are set the way they should be.
Members in different usergroups have mentioned this as well.
Members are only getting alerts on Tags, Likes and Quotes.
The only checks are really surrounding having already received an alert (e.g., for a quote), whether the user has chosen to opt-out of the alert, whether the post was by an ignored users, or whether the thread was already unread.
Beyond that, an add-on is the only thing I can think of; this isn't a problem I've heard of before. Please see if you can confirm the issue with all add-ons disabled.