Hi,
I seem to be having a similar problem. I think I'm toward the end of Act III. I've got old quests that I've finished, like the merchant's amulet and dealing with the two assassins that are still showing. I have new quests that never appear in the log. While some new quests have been added, then cleared when finished, just as they should be.
I wonder if there is a problem if you don't finish the quest quite the way that was intended. For example, when I gave the merchant back his amulet, he took it, rewarded me, then cried out that it was cursed and snuffed it! Was I supposed to somehow lift the curse first? Also I killed both assassins in the end (never liked backstabbers) so maybe the game thinks I haven't finished the quest 'cos I didn't do what the quest originally asked. Or hey, maybe it's just a bug!!
Great game though.
Paul