I believe this is the same bug reported in UE-20326.
“Using the Show Mouse Cursor command (or BP node) will make the mouse appear in the game window however at that point the mouse does not interact with the game unless one of the mouse buttons is held.”
I am experiencing this with both the default and a custom (BP) PlayerController. The Show(Hide) Cursor checkbox of the controller seems to be the culprit; although the issue will also appear using a ShowCursor node in the PlayerController blueprint.
In my experience, this has shown up in a project started using the FPS template.