Nether quartz appearing, Player changes to the Nether world got wiped (minecart, torches etc) and "breaks" level.dat (HDD too busy, system hang)

I've noticed that Nether Quartz Ore started appearing with 13w10a in my world. I have a rail going to a far Nether fortress and the ore appeared under it as well. In few blocks distance everything I created or changed was reverted back like I've never been there before. Also, HDD went crazy, system and minecraft hang. Ghast was stuck in the ground near there as well.

I tried to fix it by rebooting computer / restarting minecraft server a few times but had no luck.
I reverted back to 13w09c but the damage was already done.

While I had the Nether problem, the normal world was completely fine

Fortunately, I create backups every day so I could replace the damaged one and now everything's fine on 13w09c.

Sorry, guys I'm new here. Not really sure if this is the correct way of reporting a bug. I'm happy to answer any questions or create screenshots in the undamaged world if needed.