When I did my T-rex project, I set up a series of blend shapes to alter its facial expressions. Before I explain the problem, let me show you a picture of the model's head.
The blends worked well except that they did not follow the influences of the skeleton that the model was bound to. If the Rex's mouth was opened and I "morphed" his face into an angry expression, his mouth would close. Should that happen? I think that the blend shapes should follow the deformations caused by the skeleton but I don't have enough experience to know for sure.
One thing I can think of is that I created the blend shapes (copies of the head) before binding the model to the skeleton. I also "un-bound" the model several times during the rigging to adjust the skeleton.