The overlay with t value has precedence over other overlays. If the problem occurs, I can run the following function, and it will get fixed in existing windows. However if I create a new window, it will show only text. If I press + in that window, a new overlay will be created. Perhaps the t overlay was meant to be the default, and someone misunderstood it's effect.
(defun 13887-fix-helper1 ()
(interactive)
(let* ((ovs (overlays-at (point)))
(ov-t (find-if (lambda (ov) (eq (overlay-get ov 'window) t))
ovs)))
(when ov-t (delete-overlay ov-t))))
Here is one more helper function which might be useful.
(defun 13887-own-overlay-present-p ()
(interactive)
(let* ((ovs (overlays-at (point))))
(find-if (lambda (ov) (eq (overlay-get ov 'window)