How long were they on Science Diet? I would never feed Science Diet to any dog, especially those used for breeding. Most all the Science Diet has soy in it and soy has been linked to reproductive problems. My in-laws that raised Border Collies were feeding a dog food with soy and their females hardly ever came in heat. What brand of Nutro are you feeding? My personal opinion is that Nutro is not a very quality food either. I know some of the Nutro has soybean oil. I really recommend you get your dogs on a quality dog food (no corn and no soy).
Here is some information on the dangers of soy:
http://www.shirleys-wellness-cafe.com/soy.htm
Now it is possible that this has nothing to do with diet and maybe just the timing of your breedings. How old are the females you are talking about? Some females as they get older starting releasing their eggs later in their cycle. So say your are breeding on the 9th, 11th and 13th days and she releases her eggs say on the 16th day then it is possible to miss her.
I hope this was helpful, there are no simple answers.