I was just playing it tonight and I noticed this. It's part of Thaumcraft and I don't have Optifine installed. Have no crashes and everything else is working.
When I entered an area with a lone tower. I don't know what tower that was, but it had some phantom floors and hidden spikes. I deleted my save and made a new world and when I fount another tower...same problem.
OK. I disabled all the mods except for Thaumcraft and the area that is invisible is the Taint. It rendered OK with just Thaumcraft running. Trying now to find out what other mod is causing this.