To go along with the long portal transitions, I have found that in my survival world, when I come back to the over-world from the nether, certain chunks just don't load. Also the loading screen during the portal transitions says Generating World and Building Terrain. The chunks when I return only show entities, no blocks are visible just entities and void. I discovered it fully when I went to the nether for about a minute for lava, then came back and the portal took slightly longer than usual to load and my storage system was not loading and I had to re-log to fix it. It has also happened several times with a different chunk in the nearby area.