Not getting progress towards dungeon level achievements
Solution 1:
The Torchlight achievements are generally buggy. I had quite a few problems with them myself, most of the time exactly like you describe it - a counter stopped working. (In my case it was for sold items and killed trolls, if I recall correctly.)
So you're not alone (look e.g. here), and there probably isn't much you can do. :(
Edit: It just occured to me: saving achievements doesn't seem to work when you're offline. But somehow I presumed that would not be your case.