Android button setPressed behavoir changes when AlertDialog is active

Question

I currently have a button which is setPressed(true) on an app i'm creating. I also have an AlertDialog box appear when I press the back button. I noticed that when I press the back button and the AlertDialog box appears the button I have set pressed to true changes to false. I can't understand what is causing this as there is nothing in my code to tell the button to change setPressed to false. I can supply my code if anyone wishes but I believe something else causes this. Any help would be hugely appreciated. :)

public boolean onKeyDown(int keyCode, KeyEvent event) {

    if (keyCode == KeyEvent.KEYCODE_BACK) {
        exitByBackKey();

        return true;
    }
    return super.onKeyDown(keyCode, event);
}

protected void exitByBackKey() {

    if(!instOn){
        if(toast != null) 
            toast.cancel();



        AlertDialog alertbox = new AlertDialog.Builder(this).setMessage("Do you want to exit?")
                .setPositiveButton("Yes", new DialogInterface.OnClickListener() {

            public void onClick(DialogInterface arg0, int arg1) {

                finish();
                System.exit(0);

            }
        })
        .setNegativeButton("No", new DialogInterface.OnClickListener() {

            // do something when the button is clicked
            public void onClick(DialogInterface arg0, int arg1) {
                 if(!stage1 || !stage2){
                     button3.setClickable(false);
                     button3.setPressed(true);
                 }
            }
        })
        .setNeutralButton("Restart", new DialogInterface.OnClickListener() {

            // do something when the button is clicked
            public void onClick(DialogInterface arg0, int arg1) {

                newGame();
            }
        })
        .show();
        //alertbox.setCancelable(false);

    }
    else{
        instOn = false;
        trans.transition.reverseTransition(800);
        popupWindow.dismiss();
        button1.setClickable(true);
        button2.setClickable(true);
        soundButton.setClickable(true); 
    }
}