I am writing to the org-mode list first, because I have only been able to reproduce this problem in org-mode.
With a recent Emacs master build, faces can have the :extend t property to indicated that they should extend after the newline. This is useful for a user to customize, eg, for `org-block', and it also applies to default faces like `region', `highlight' or `secondary-selection'. Using this with a current elpa pkg of org-mode, and setting :extend t on faces like `org-block`, "often" the cursor vanishes at the EOL of a line using such a face. It reliably happens for `org-block', only sometimes for `secondary-selection'. Has anybody else experienced that as well, or do you have any pointers on how to further investigate this? I think I remember that org-mode does something with text overlays, but I can't relate that to what I see. There might also be an issue with face inheritance and the new :extend attribute --- I might post on emacs-devel to get a better idea of that as well. Thanks, Ingo