Players adjust differently. A good case is NYM prospect Carlos Gomez. Youngest player in AA this year. Take a look at his stats:
Monthly splits show how lost he was to start the year, then wah-lah! He started figuring it out in June, had an outragous July, and a solid August. If you look over his career he's struggled at lower levels too. He is similar to Stubbs in that he is very toolsy. Sometimes the toolsy players take longer to develope, but when they do they are exciting ballplayers.
Don't give up on Stubbs yet guys... his ceiling is pretty high for a prospect, even if the tools have yet to translate to results.