Why does my dog only like one of my sons, but not the other?

My first son was maybe 1.5 years old when we got Sy. Sy is an Alaskan Husky / Blue healer mix. She's a rescue dog, but we got her when she was still a puppy, about 6 months old in fact. Before we brought her home we had my son meet her and her disposition was wonderful with my toddler always remaining careful, even as a puppy, not to knock or bump into my first son. At the time that we got her I was pregnant with my second son. Things were great until the second boy started to crawl. At first my dog would just growl, yap, and run away when the second approached her. She won't have anything to do with my second son (he's now 2.5.) It seems as though her distrust in the youngest boy is affecting her tolerance for the oldest whom is now 5 years old. She's super loyal to me, she's my shadow. I noticed she's starting to let my eldest throw her the ball. But it just saddens me that my sons won't get to experience that lovely bond that I had with my German Shepard dogs when I was growing up. I lived on the floor with my dogs! Sy has nipped at the boys when they're being too rough with her. They since have learned to play soft with her and not to take it personally if she nips at them. When she nips, it never hurts them, it just shocks the kids and they feel insulted, (if that makes any sense.) How can I change her feelings towards my kids?