Different integral membrane proteins will be soluble in different
detergents, the addition of SDS to a buffer containing Triton X or NP40
will often solubilize more than either detergent alone. Also, Empigen BB
is able to solubilize proteins that are associated with the cytoskeleton.
The insoluble material left in your preparations is probably the
cytoskelatal fraction and can be removed by a additional high speed spin.
Keep in mind that membrane preparations are generally used as steps towards
increasing the relative purity of a sample more than for optimal recovery
of a protein (it's a trade off, decreased yeild for increased purity).