syndic

Got a fix for you to try: Try /time add 999999 and let me know if that does it for you.

I have also been unable to repair the damage done.

I can confirm this in my case - using the NEI time changer stops water flowing in the chunk I'm in.

Trying to narrow it down, have you been using redpower deployers in that area?

I've had the same bug, first noticed it around the cooling pools of my nuclear reactor. Luckily it was defuelled. Anyone got any suggestions? Was your world a converted 2.1?