I’ve noticed something similar, where tag notifications are not working at all. I only discovered it when wondering why nobody was replying to a post and then digging around in the email logs.
They are not appearing in the users’ Notifications–>Tags at all, and are not being applied. This is also the case with safe-mode on.
When interrogating the database, they seem to be correct.
I’ve had to do an ugly workaround with @mentions instead.