OK, that is going to be tricky to describe and perhaps to recreate but it has been with V5 from early stages.
I have a few polysurfaces which I convert into meshes.
321 meshes added to selection.
I run Command: _ShowEdges,
Found 234 edges total; no naked edges, no non-manifold edges.
I then Export to stl,
luckily i have the prompt active and get the error message that there open object in there. looking more carefully I find and fix.
I know you are probably going to ask me for a sample, but it will be of no use, when I open it in a new instance of rhino I cannot replicate the bug.