After the snapshot update, the server shuts down reproducibly when a player enters a nether portal. The server log looks normal, and from client side it looks just like the server was shut down normally.

L3viathan delivered reproducibility instructions:

How to reproduce:
1. Create new world
2. Enter Nether
3. Attach Item Frame to block
4. Put Item into Item Frame
5. Leave Nether
6. Reenter Nether

P.S.: This can also be used to dupe items: Place an item in the item frame and break the chest.
P.P.S.: It might have nothing to do with the chests, just with the item frames