From emacs -Q:
M-x global-hl-line-mode
then open a file and move around with C-n

Text at the current line disappears seemingly at random. It comes back
eventually and/or if I do C-l.

It does this regardless of major mode and I experienced the behavior in
24.5 and 25.1




In GNU Emacs 25.1.1 (x86_64-unknown-linux-gnu, GTK+ Version 3.20.9)
 of 2016-09-18 built on juergen
Windowing system distributor 'The X.Org Foundation', version 11.0.11804000
System Description:    Arch Linux

Configured using:
 'configure --prefix=/usr --sysconfdir=/etc --libexecdir=/usr/lib
 --localstatedir=/var --with-x-toolkit=gtk3 --with-xft
 'CFLAGS=-march=x86-64 -mtune=generic -O2 -pipe
 -fstack-protector-strong' CPPFLAGS=-D_FORTIFY_SOURCE=2
 LDFLAGS=-Wl,-O1,--sort-common,--as-needed,-z,relro'

Configured features:
XPM JPEG TIFF GIF PNG RSVG IMAGEMAGICK SOUND GPM DBUS GCONF GSETTINGS
NOTIFY ACL GNUTLS LIBXML2 FREETYPE M17N_FLT LIBOTF XFT ZLIB
TOOLKIT_SCROLL_BARS GTK3 X11

Important settings:
  value of $LANG: en_US.UTF-8
  locale-coding-system: utf-8-unix

Major mode: Org

Minor modes in effect:
  global-hl-line-mode: t
  org-indent-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  tool-bar-mode: t
  menu-bar-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  line-number-mode: t
  transient-mark-mode: t

Recent messages:
For information about GNU Emacs and the GNU system, type C-h C-a.
Global Hl-Line mode enabled

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message rfc822 mml mml-sec
password-cache epg epg-config mm-decode mm-bodies mm-encode mail-parse
rfc2231 mailabbrev gmm-utils mailheader sendmail rfc2047 rfc2045
ietf-drums mm-util help-fns help-mode mail-prsvr mail-utils cus-start
cus-load hl-line org-element org-indent org-rmail org-mhe org-irc
org-info org-gnus gnus-util org-docview doc-view subr-x jka-compr
image-mode dired cl-loaddefs pcase cl-lib org-bibtex bibtex org-bbdb
org-w3m org org-macro org-footnote org-pcomplete pcomplete org-list
org-faces org-entities noutline outline easy-mmode org-version
ob-emacs-lisp ob ob-tangle ob-ref ob-lob ob-table ob-exp org-src ob-keys
ob-comint comint ansi-color ring ob-core ob-eval org-compat org-macs
org-loaddefs format-spec find-func cal-menu easymenu calendar
cal-loaddefs time-date mule-util tooltip eldoc electric uniquify
ediff-hook vc-hooks lisp-float-type mwheel x-win term/common-win x-dnd
tool-bar dnd fontset image regexp-opt fringe tabulated-list newcomment
elisp-mode lisp-mode prog-mode register page menu-bar rfn-eshadow timer
select scroll-bar mouse jit-lock font-lock syntax facemenu font-core
frame cl-generic cham georgian utf-8-lang misc-lang vietnamese tibetan
thai tai-viet lao korean japanese eucjp-ms cp51932 hebrew greek romanian
slovak czech european ethiopic indian cyrillic chinese charscript
case-table epa-hook jka-cmpr-hook help simple abbrev minibuffer
cl-preloaded nadvice loaddefs button faces cus-face macroexp files
text-properties overlay sha1 md5 base64 format env code-pages mule
custom widget hashtable-print-readable backquote dbusbind inotify
dynamic-setting system-font-setting font-render-setting move-toolbar gtk
x-toolkit x multi-tty make-network-process emacs)

Memory information:
((conses 16 162162 7289)
 (symbols 48 27365 0)
 (miscs 40 271 655)
 (strings 32 37912 6108)
 (string-bytes 1 1137387)
 (vectors 16 18378)
 (vector-slots 8 502578 5776)
 (floats 8 213 90)
 (intervals 56 1847 0)
 (buffers 976 19))