Looking at the replay, I think the only one who was confused was Cundiff. I think all the players on the field knew it was 4th down, and so did the coaches. After the third down play, there is only a slight pause, and then Nantz says, "and the field goal unit is coming on to the field." But Cundiff apparently didn't come on with them. He comes running out with about 17 seconds left and gets to the spot with about 12.
So, I think it's legitimate that the scoreboard mistake confused Cundiff. He might have looked up and been confused, since he's concentrating on his practice kicking. Also, while coaches are supposed to get him ready, you also generally leave a kicker alone in that circumstance. In fact, I not only think this story is plausible, but it explains why he came out to the field late.
I think most of the points being raised in this thread are good ones -- that they had a time out and also that 17 seconds is plenty of time for a kicker to make a chippie. Still, I think there's a bit of a gripe here. But in the end, he missed it and that's that. I don't think there was malice on anyone's part. It was just a weird series of events, started by the fact that the fumble doesn't advance. A mini-break for us. That's football, and I have no problem admitting it.
One issue that nobody is talking about is whether the clock should have kept running after the Boldin fumble. Even though the fumble can't be advanced, I don't understand why they didn't stop the clock, since it went out of bounds. The refs were confused -- they were acting so carefully to mark the ball at the spot of the fumble, I didn't see either give a wind the clock or stop the clock signal. I think the result was correct -- since the fumble can't advance, I guess the play is over in bounds and the clock properly kept going. I thought it was interesting though. There was clearly referee confusion there. Typically, it's the job of the R to signal down, and the scoreboard operator does nothing but watch the R to decide what to put up. He's not looking at the chains or the monitor or any of it. You can't see Riveron on the tv replay, but it would be interesting to see the all angles camera.