At a guess you had the blendShape node after the skinCluster node in history?

When making blendshapes for a rig, the blendshape node must be before the skinCluster node in history or else it will remove the deformation from the joints, which sounds like the problem you had.

If this was your problem, make sure when you make a blendShape node that the Deformation order (found in the advanced tab) is set to `front of chain`.

Richard