The SKS on my 2005 Prius stopped working recently. The pushbuttons on my fob will lock & unlock the doors, and I can put the fob in the socket to start the car. But the SKS won't lock when I push the black buttons or unlock the doors when I touch the handles or start the car when I push the start button. At first I thought it was the "KEY" switch under the steering column, but I've tried switching it on and off a dozen times, but still no luck. I would try the other key fob, but I also recently lost it. I thought for a moment that perhaps I lost the fob inside the car and that's why it won't lock/unlock with the SKS. That would make sense. We've experienced that scenario when my wife puts her purse containing the fob in the cargo compartment and I try to lock the doors from the outside with the black SKS button. But I would think that even with the lost fob in there, I'd be able to start it with the SKS. Right? Afterall, I've never had any trouble when my wife had her fob in her purse and I had my fob in my pocket. Or does the location inside the car matter? So that leaves the possibility that the fob is somehow broken in such a way that the SKS doesn't work but the pushbutton does. Would a low battery behave like that? I intend to replace it as soon as I can find a tiny screwdriver. ...Or possiblity that there's something broken on the car. I'd rather not think about that possibility. Any thoughts on this would be MUCH appreciated!
Easy fob battery test: when you push any button on the fob a small red light should flash. If not, replace the battery. You will need a tiny screwdriver to do this.
I think you may be onto something with the lost fob...I can't recall if you would still be able to start with the lost fob in the car, there's an eventual time-out that will prevent you from starting with SKS, but I would think that that would reset once you opened the car. My money, like the others here, is on the battery being bad too. Often there's enough juice for the buttons to work but not the SKS as the battery is about to die.
Re: Lost Fob in Car - I know from prior experience that there are areas in the car that the fob cannot be sensed. I found this out on a trip when my GF had one fob and I had the other. We stopped for a break and could not lock the car. It was because my GF had left the fob in her purse inside the car. But at another stop, the car allowed me to lock it with the fob inside. IIRC correctly, the "blind" area was behind the passenger seat on the floor. So the missing fob could be in a "blind" area in the car.