Michel, it is the order in which the addons are stored in the database. It works perfectly for me since I have installed the Smilies Addon AFTER the Reply To Comments Addon.
You can try to remove the Smilies Addon from your Addon folder, go to your Addons page and make sure that it isn't there anymore.
Then upload it again into the Addon folder, go to your Addons page and see if it is in place.
Now it should be found after the Reply To Comments addon and replace the smilies correctly