Hi, I'm not sure why you are having problems. Perhaps it is only related to the dual camera setup. ?
I have not found any problems with starting the camera after the program, or vice versa. My only issue is that it does not let you know when the camera is NOT connected.
I installed NCC two days ago, and have been taking nearly 3000 photos a day on my D3S with it since, and no hiccups. Its very fast for me, just like the nikon software... and unlike the nikon software, it hasnt crashed yet haha