I have had this problem for quite some time now, Where alot of players complain about the chests in their chunk were all gone, in addition some spawners return to the minecraft default type (Pig) , All the plugins on the server are customly made and they are all made by us, The developers we use absolutely no publicly published plugins, None of our plugins mess with the chunks, not loading and nor saving.
We only sometimes use the chunk x and z coords for claims but yeah that wouldn't cause such issues..

Our players complain saying that when this issue occurs a huge lag spike occurs as well, We don't see any errors in the server logs nor in the console relating to this issue.

We are also using the spigot version 1.8.8 the latest build.