> I have a org document that, when I navigate through it, the org-mode menu disappears and reappears.
> ...
> polymode

This.
Major mode menu is displayed only when the major mode is active, but
polymode will switch the major mode depending on the point location in
the buffer. Most likely, you see the menu disappearing when moving
inside src blocks where polymode activates another major mode.

(Please excuse the html reply – I needed to include snapshots and thought this the best way)

Indeed, I am delighted when polymode works in this fashion, as designed.   However, I am finding that the menu is changing when I navigate between org headers, such as below when I hit a single down arrow to advance from “** DONE publish help.md markdown as helptext in sidebar” to “** DONE remove custom search builder”. 

Thoughts?