I have experienced the same issue, while watching the DOM it seems like the link modal is constantly showing/hiding. (The DOM element keeps flashing on each change).
I’ve added some custom CSS to fix the z-index problems, but the flashing (hiding/showing?) means it’s not really fixed.
It only seems to occur for new links. If you swap the WYSIWYG to text mode, add the HTML for a link and then swap back to visual, you can edit it the link fine (as long as you have the z-index fixed).
Not sure if that’s useful information, but that’s as far as I got with it.
