Never mind. Things are a bit different in phpBB 3.1.
This is from the FAQ section.
What is the difference between bookmarking and subscribing?
In phpBB 3.0, bookmarking topics worked much like bookmarking in a web browser. You were not alerted when there was an update. As of phpBB 3.1, bookmarking is more like subscribing to a topic. You can be notified when a bookmarked topic is updated. Subscribing, however, will notify you when there is an update to a topic or forum on the board. Notification options for bookmarks and subscriptions can be configured in the User Control Panel, under “Board preferences”.
Seems like the difference now is that subscriptions can be applied to topics and forums, while bookmarks work with just topics.