If you add a field to the media/attachment field and set it to be a WYSIWYG editor, then click the ‘link’ button in the toolbar, the popup is under the modal.
I know it’s probably a wordpress thing but I thought it best to report it anyway. 🙂
I will mark this thread for the developers attention.
You might also want to open a new support ticket as that might be a faster way to get the developers attention on this bug. http://support.advancedcustomfields.com/new-ticket/
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.