I wrote a long time ago about how to do cross sections in Rhino. I mentioned that it needs to be Object intersection. If you do Boolean Intersection, this technique is not going to work. I found that the earlier instruction might have been a bit confusing because there are multiple ways to do intersections in Rhino.
The original article is here: http://designaplane.blogspot.com/2008/10/irhino-learnings-of-today.html
Please read it.
The function what you have to use is Intersect (to do Object Intersection).
If you type it to the command area, type Intersect, not Intersection or Booleanintersection.
You know that you have chosen wrong intersection method if you have to select two set of objects. Multiselect everything (your cutters and the lofted surface) at the same time and do Intersect. It works.