It seems that there are cases, there the addition of the new PK to
site_setting breaks the updater.
Can you make sure to drop every possible present PK before adding the new PK?
I've looked over all updates. In this case it looks like the user skipped an update (eg when executing SQLs manually or for some other reason). The table that was added in 3.0.0-b1 did not have a primary key. I don't think there's much to do here as it should be edge case. Haven't heard anything similar from another user, and if so, it should be easy to fix I suppose.