After some research, it seems there is a difference between phpBB 2 and phpBB 3. In 3, they changed the mark-read behavior to "every post is unread until marked read". It is switchable.
Under Load Settings -> General Options:
Enable server-side topic marking: One of the many new features phpBB3 offers is server-side read tracking. This is different from phpBB2, which only offered read tracking based on cookies. To store read/unread status information in the database, as opposed to in a cookie, select Yes.
But it seems most people like it like this, and if everyone is used to it, it's probably better it just stays the way it is.
At least I know why now..