My guess is that they tried to roll out a change, that failed, so they did a roll back and attempted to rerun a script which populates the last few transactions in the points journal, however that script had a bug which has caused multiple inserts.
Since multiple inserts can be very difficult to detect in a large database they are right now trying to work out how to roll back the changes before they roll the current set of points changes into the journal. The (most likely) reason that the points balance is still accurate (from the other day) is that they have stopped doing roll ups of the points journal.
If my guess is correct, this is actually a very difficult thing to repair, and they have likely caused a lot of damage to their database. So I wouldn't be expecting points to be posting from flights in any time soon.
I would recommend that you keep boarding passes until they get this issue sorted, since they may actually lose records out of this, so you'll need the paper \ photo'd version to verify you actually took the flight.