This occured in Nightmare.

After killing Belial, I went on to act 3 for about 5 minutes. I then left the game and joined another player's game in act 1 NM. After I left that game, I was unable to continue in Act 3 and had to kill Belial again.

Furthermore, my checkpoints in the last two quests had been erased.

EDIT: A relevant detail may be that I never reached a checkpoint in Act 3 before leaving.
Edited by DFxEvac#1952 on 5/17/2012 11:33 AM PDT