Hi Eli,
See inline.
I used Emacs26@078fb7f6df4178d5a35243dad164cdd196392e71Cc: 27647@debbugs.gnu.org, jonaswestlund101@gmail.com, npostavs@users.sourceforge.net From: Romanos Skiadas <rom.skiad@gmail.com> Date: Wed, 11 Oct 2017 21:32:06 +0100 echo "foo" > /tmp/test.txt (cd /tmp && git clone https://github.com/emacs-evil/evil) Add this to a file, eg /tmp/test-init.el: (add-hook 'text-mode-hook (lambda () (display-line-numbers-mode))) (add-to-list 'load-path "/tmp/evil") (require 'evil) (evil-mode 1) emacs -Q -l /tmp/test-init.el /tmp/test.txt Put this in the test.txt buffer an eval it: (let ((overlay (make-overlay 1 6 nil t nil))) ;; flyspell does this on misspelled words (overlay-put overlay 'help-echo "a")) Make sure you are in normal more (press ESC) Move the mouse above the f at the start of the buffer and hover until the "a" shows up. Click and drag along toward to end of the line. The line numbers consistently go away with this recipe for me.Doesn't happen here with the latest emacs-26 branch. Are you using that branch, or are you using some other code base for Emacs?
As long at that is the latest evil, which is what I tested with, that shouldn't matter(I didn't clone the evil Git repository; instead, I downloaded a zip archive and unpacked it on my system. I don't think it should matter.)
It is indeed a GTK3 build and setting x-gtk-use-system-tooltips to nil does indeed make this problem go away. I've set it to nil on my init file for now.Can you tell the details of your build? If it's a GTK build, does the problem go away if you tell Emacs to use non-GTK tooltips (by setting x-gtk-use-system-tooltips to nil), or if you turn off scroll-bar-mode?
I'll start dissecting evil to see what causes this.Thanks.