hmm, what do you mean flipped UVs? do you mean the normals? i checked there a while ago and the normals are OK, the UVs are layed out like the normal map is.
i thought of something, the envelope works bothsides? like to the outside of the mesh and to the inside? or the percentage you give to check for geometry only works for the outside? because on the last example i posted it seems the NMap is missing those interior faces. :S and even on the High poly mesh the normals are OK facing outwards the mesh