Windows 7 SP1 64b, Java 8u112 64b
I played with different world generation parameters, then teleported around in creative mode to several different locations in a radius of about 2000 blocks. Then I tried to render the saved regions with TMCMR - TOGoS's Minecraft Map Renderer. I was confused to get a huge but mostly empty map with single blocks (or columns) in very distant regions. So I looked into the saves(mapname)\region directory.
It contained not only region files for the closer range around the origin (r.0.0.mca), as expected – r.[-5..4].[-5..4].mca – but also occasional random exceptions:
and many more (all negative X, positive Y; all 12288 bytes). So I wonder if the world generation possibly does not initialize some parameters correctly and accidently stores generated blocks (columns) into completely wrong chunks.