Okay, so I followed these steps, and it fixes the shoulder problem, but now the head is doing it instead and not moving up along with the rest of the model...
Here are the steps that I followed:
"Select your main mesh. Go to Modify->Evaluate Nodes and select "ignore all." In the Rigging toolset go to the "Skin" tab -> and "Go to bind pose" From here you will have to re-duplicate the mesh to remake your target blendshape. Make sure Pre-Deformation is set in the "Blend Shape" tool settings. Afterwards you can go back to the tabs in the first step to reevaluate the nodes on your main mesh."
Does anyone know how to fix this problem?