It is not uncommon for pups to have murmers and then the murmers close up. It depends on the type of murmer whether or not they close.
Our big boy has SAS and it wasn't found until later. And yes he was checked several times. It was just missed. He was 6 months when another vet said, "Hey wait a minute" and had us fly to Seattle to see a cardiologist. Sure enough...it was not a good thing.
Most of the time murmers are worried about after 13 to 14 weeks of age I believe. That is when you can go to a cardiologist to find out if it is functional or not.