Items are disappearing in chests, so far known with the double combined chest. the items in the bottom half of the storage would suddenly disappear. I also had noticed if a player logs out and back in slabbed and really closed up zones, that their items could disappear as well.

Another potential bug is how the Enchanting Table does not get empowered by the Bookshelves, Raw Cod and Cooked Cod would not become consumeable for some reason.

I am operating in the "INFINITE WORLD" setting as well with 12 chunks.