I came back to this problem again today. I've done sectioned work in the past, and I thought I'd just translated the model up through the stock area, using top/bottom of part to control the toolpath. So, I tried it in V25, just as a sanity check. Same issue there as I saw in V26, so it's nothing new or related to DMS. Apparently, I just sectioned the model as needed, last time.
Don, this is an easy thing to do with a "regular" solid, in BobCAD, but you'll need an external slicing tool, such as mmoe discussed, to handle slicing a .stl mesh. Frankly, you'd be doing yourself a favor by spending time with the solid modeling tools in BobCAD. They're not the best, but they give you lots of options, as in this case, that a mesh just won't. When you rely on "found" files, you're locked into whatever baggage they come with. BobCAD, like a lot of other packages, is limited in its ability to manipulate meshes. Some things, it handles well. Others, not so much.
Luke