The unit frames were moved but that's about it.

Toggling some of the prefs and pressing OK (at which point the UI reloads) makes no difference.

Fixed by manually installing (don't use WoWMatrix).

Hmm, I don't condone the use of WoWMatrix as I have honestly no idea how it has ended up there. Maybe they poll from WoWInterface but here and this repository are the only official sources.

Note: The build that WoWMatrix has supplied you is a rather old build. Please update via WoWInterface.