I’m a brand new APM owner and also case owner. Unfortunately also another one affected, I love this case so much I’m going to try get Apple to swap my APM with another.
Another observation from another perspective. The APM does not wake up in the morning is because after being placed in the case, it still attempts to connect and disconnect in cycles (observe your Bluetooth settings). After a number of cycles the APM locks up. Another indicator is the Battery widget will appear to report on the APM battery but it's actually not a live reading because your APM is already locked up.
This is almost like the case magnet is there but almost hitting the low power mode switch but only partially causing the APM firmware to trip. My speculation of course.
Also another note, I believe my case is Batch #24 and the magnetic butterfly looks very different from all the photos posted online. The butterfuly also sits a lot lower - have no idea if this is going to be any different.
Update:
Have reached out to Apple, they are replacing my APM with another unit, we shall see with my replacement if this is still the case.