Chunks behave weirdly in following ways if they are empty when server is loaded (might be only client):

• Blocks placed in these chunks don't render. This also applies to special TE renderers. Bounding box does render as shown in screenshots. It also seems as if these blocks instead of rendering in their own chunks render in nearby chunks that also don't contain any blocks. It only renders them and they are not actually there, so player can pass trough them.
• When player exits and enters the world in one of these chunks his position can't change unless teleported out, camera rotation works fine however.
• If a block is placed in one of these chunks and player exits and enters the world the chunk starts behaving properly even after removing all blocks in it, it still behaves like is should but upon re-entering the game they break again.
• When player enters these chunks, the whole screen gets darker.
• If player teleports himself/herself into block-containing chunks after logging in in one of these chunks, he can move trough them normally, but if he tries to teleport somewhere else in the same empty chunk or another empty one, he/she still can't move.
• When one chunk is fixed by placing blocks in it and exiting and entering the world, all of the vertically parallel chunks seem to get fixed.
• Players slowly fall in these chunks as they do in unloaded ones

I think this has something to with world saving because it gets fixed as soon as some data is stored in the broken chunks. Another thing that lead me to that conclusion is the fact that these chunks seem to be linked somehow in the client as if server is making the client think that they all share the same blocks when they get placed in one of them - they aren't rendered in the correct one, but in all of the other empty chunks they do get rendered. Screen getting darker and players slowly falling in these chunks makes me think that server doesn't even send data about these chunks to client because behaviour seems similar to behaviour you get if you enter unloaded chunks in laggy worlds/servers.

This also seems to be a new bug as I didn't come across these problems few versions back (before 1.9 snapshots).

Steps to replicate:
Create a superflat world with 1 air layer ( 3;minecraft:air;1; ).
All chunks should behave like this and when you enter you will not fall into void as you should, you will just be stuck in mid air because of the weird behaviour.

Picture descriptions:
First picture - Bounding box seems to render properly, but blocks don't.
Second & third pictures - Screen gets darker as player enters these chunks.
Fourth picture - Surrounding empty chunks seem to render blocks that aren't rendered in the chunks actual blocks were placed in.
Fifth picture - Blocks are only rendered and player can get trough them, they aren't actually there.

This seems similar to MC-56917, but that seems to apply to cubic chunk rendering (and is closed) and my bug seems to be related to world storage format.