You’ll have to check your xnormal settings, make sure it’s set to bake the right kind of map (‘bake highpoly vertex color’) and that the highpoly mesh isn’t set to Ignore Per-Vertex Color. The mesh will also have to be exported to OBJ with polypaint on.
An alternative, older method is to give the highpoly a temporary set of auto UVs (such as GUVs), bake the polypaint to that, and use Xnormal or any other 3d app to bake the texture from the sculpt to the new mesh (in xnormal it would be the base texture to bake field in the highpoly options, along with the bake base texture map type). This particular technique can be seen at http://eat3d.com/free/zbrush_xnormal
Otherwise, you’ll have to subdivide the new mesh in order to have enough verts to handle the polypaint data, and use Project All with RGB on, then create a texture from polypaint if all goes well.