<Dang, posted too slow.Oh well, leaving post intact>
You can't extrude the bottom 3D pline because it's not coplanar. That is, all vertices do not reside on the same plane. This might be because each vertex (corner) represents a ground elevation rather than an idealized plane </guess>.
One quick (non programmed) solution is to set the coordinate system to WCS, and trace over the 3D Pline with a 2D pline, then extrude the 2D pline. Note that the first vertex you pick when creating the 2D Pline will define the z coordinate for all vertices that follow.
If you provide a sample with a greater number of samples it would be easier to suggest an automation route. I'm reluctant to pursue that route on the basis of two entities.