There are several courses on WGT that have multiple pins per hole. BPB, St Andrews, Oakmont for sure. I also think that Congressional has 2 sets, since in a CTTH game there are pins that you don't see in stroke play. Not sure about RSG but I know that Kiawah only has one set of pins.
The random nature of these is what I wonder about. I would assume that would mean that you see them equally. However on some holes, St Andrews 11 for example, I have never seen the up pin placement in stroke play. Other pins appear rarely, while some holes for example St Andrews #1, you see the up as well as the back fairly equal.
Why don't we see them in a really random fashion?