Hi Mike, is it the Construct > Offset > Inset command that you're trying to use for the "Nut" function?

Inset can sometimes tend to get confused when you use it on a piece that is smooth to the surrounding pieces. That's because it normally tries to shrink the boundary around the surface by using offsets of the surrounding adjacent surfaces, but that method does not work when the surrounding surfaces are smooth, so in that case it tries a different technique but it's kind of unreliable.

The next version of the geometry library is having some work done to its shelling/offset function so I have some hope that will get improved.

Meanwhile see this thread for some other techniques that can be used instead:
http://moi3d.com/forum/index.php?webtag=MOI&msg=3859.1

For something like this you may want to divide the object into 2 different solids (that are each capped) by cutting the full solid object by a dividing curve using boolean difference, and then fillet or chamfer the edges.

- Michael