When you use the intelligent key are you still getting the accessory functions like radio etc? or are you getting no response from pressing teh start button?
Then it's a problem with the key recognition and that could be from the key fob itself.
The fact that the second FOB works only confirms that.
More than likely since the other FOB works sometimes, it did not lose its registration, but instead the FOB itself is bad preventing proximity recognition. Since you already changed the key battery, that FOB will likely need replaced, but the dealer can use the remote checker to verify prior to charging you for a new unit.