This is a guess but it sounds like it could be your deformation order, you might need to set it to Front of Chain.

Here is what the Maya help files say about it.....

Front Of Chain

Front Of Chain is only available for blend shape deformers. Blend shape deformers are typically used to create deformation effects on a skinned character. Front Of Chain assures that blend shape deformation effects occur before the deformation effects provided by the skinning. If the effects occur afterwards, undesirable double transformation effects occur when the skeleton is posed.