Toyota Repair: Door locks and key less entry 2002 Toy Sienna, key less entry, door locks

Question
I have a 2002 Toyota Sienna Van.  Whenever the key is in the ignition and the front passenger door is open, all the door locks, except the driver's pulsate twice and there is an audible click (twice) below the steering.  My key less entry and remote does not work.  The batteries are new in the remote. To lock and unlock the doors I have to use the keys.
What causes the door locks to click twice when the key is in the ignition and the passenger door is open?
Could this problem cause the the key less entry to not work.  
I have the procedures to reset the key less entry codes for the Sienna, but it will not reset.

Answer
Yes it will cause the keyless remote not to work. Is there another aftermarket alarm on this van, look below the left side of the dash and let me know if there is an LED there and if so what is it doing?  Flashing, on steady or off? Did you recently purchase this van? When did this start to happen. Was the car battery replaced?