Sounds like the normals are facing the wrong way. This may sound goofy - okay, it is goofy - but try Boolean Intersection or Boolean Union. In Rhino, if one object has the normals going the wrong way, you get strange results with Booleans. Before I figured out how to change the direction of the normals, I discovered that sometimes a different Boolean operation would give me the results I wanted - if not the ones I expected. See if this works. I'm kinda curious if I'm right. :-)