Hi Paul,
I believe this is a Rhino bug, not madCAM. I see this with Rhinoscripts that create layers but have nothing to do with madCAM. Sometimes they don't show up in the list, even though they were created. Next time this happens, please try the following:
1) Go to the layer pane and select Filters (the funnel icon).
2) The check mark will most likely be at "All Layers". Change it to "On layers".
3) Now change it back to "All Layers". This will refresh the list
Does your layer show up now?
Dan
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)