When the children plan to send a letter to the person who leaves the gifts, they are prevented. How does this happen?Who does it?

The kids decide to leave a note in the knothole of the Radley tree.  However, when they get there, Mr. Nathan Radley is filling up the hole with cement.  Because he's there, they can't leave the note.  When Jem asks Nathan why he's filling it up, he says,

"Tree's dying.  You plug 'em with cement when they're sick.  You ought to know that, Jem."

But as Jem discusses this with Atticus, Atticus tells him that the tree looks just fine--green leaves and all.  After Jem was by himself for awhile, Scout noticed that he'd been crying. 

"His face was dirty in all the right places."

Jem had realized that his "friend" (Boo) had been taken away from him.  He now had no chance at communicating with him anymore, and he realizes this.  Scout, however, is clueless.  She has no idea who was leaving the gifts.