Achievements not working

I am playing on survival (never creative/nothing that would prevent me from getting the achievements) and yet, there are some that refuse to show up.

I have spawned and killed the Wither.

I have used two buckets of lave in a furnance.  

I have used charcoal to make charcoal.

I have eaten two notch apples. (Yes, the enchanted ones, not just golden)