Perhaps it is related to the "fullness" of the cup, let me explain.

As you know glasses holding different quantities of liquid make differing pitches of sound, as the volume is increased so does the pitch.  How does this equate to your question?  Well by stirring the liquid you are altering the height of the liquid within the cup and thus possibly the pitch when you tap it, as you move down the cup after stirring the extra height caused by the stirring process (the circular motion / force pushing the liquid to the outside) reduces with time and thus the pitch.

Why would this be different with hot chocolate than with tea? Im not sure