Very strange, I loaded a few worlds, both with cheats on and off, not touched for a month or two.
No issues with the cheats always on, the worlds with cheats off don't autocomplete commands after opening to LAN with cheats on and the gamerules don't stick (gamemode works though)
Not sure if it helps, but the world I had that issue on had commands off. I changed it to on in MCEdit, and now commands autocomplete and gamerules actually work.
This is weird, I reopened Minecraft now, created a new world, chests show up fine. Got back to previous world, I was standing next to some chests which were still invisible, the game froze for a second and then they became visible.