I've published an update to resolve all of the compatibility problems I'm aware of. If you have a problem, please update. If that doesn't fix it, explain what's going on.
I do not have Pages, and I have not gotten any confirmation of whether the Pages conflict is still occurring, so that issue may still be out there. If so, I'll need access to someone's site to investigate. Last I hear, though, it may be a non-issue now.
What's New in Version 3.1.7
Fixed tag overriding prefix when the same value is added as both.
Fixed style changes in IPS 4.1.13 breaking multi-word prefixes.
Fixed template changes in IPS 4.1.13 breaking display of prefixes on site index.
Fixed potential errors with applying prefixes from saved actions.
Fixed tag/prefix changes from saved actions not updating the search index (profile, activity stream, search results).
Fixed possible division-by-zero error on the tag cloud widget.
Added prefix to core topic widgets.
A few issues I could not reproduce:
Prefix not showing on grid view (works for me)
Prefix input not displaying when creating a topic, with forum in prefix-only mode. (works for me)
Homepage topic feed widget -> topic titles not linking when a prefix is present. (This must have been something custom; AT&P didn't add any such thing until, well now.)
Fair warning: Most of the app will probably still work back to 4.0.0, but I will not guarantee backwards compatibility across the board anymore. It's just not worth the trouble with how frequently (and massively) things change from one release to the next. If you're running an old IPB version and you have an issue with an AT&P update, I'm going to tell you to update.