I have created a character with a selection of different face shapes to use in lip syncing. When I open up the animation mixer and load a shape onto the shape track the original face that is enveloped onto my character loses all it's envelope weighting and is not affected by the bones in the head.
It sounds like your ENVELOPE OPERATOR is above your CLUSTER SHAPE COMBINER. When you drag shapes into the mixer, your CSC should be on top of the Envelope Operator. Then, after all your shapes are in the mixer, you can put the Cluster Shape Combiner back above the Envelope Operator.