Hi supagoat, usually this kind of thing means that one of the objects has its normals oriented in an incorrect way and it thinks that the interior of the object is actually the exterior. This can happen particularly if the object has certain kinds of degeneracies like self intersecting surfaces or small loop-de-loop like shapes in trimming boundaries.
Your upper shape is kind of wonky in a few areas, it might be coming from a doing a shell on a kind of corner situation which the geometry library unfortunately handles very poorly - the sheller gets very confused when the offset shape requires a single vertex on the original surface to branch into multiple vertices on the offset piece.
The main wonky area seems to be here:
The other similar corner may be a big messed up too, probably these areas will need to be rebuilt in order to get a properly functioning solid out of the upper piece, I'll see if I can do some surgery on your object to fix it.
- Michael
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