If I'm hovering over a link in my watchlist using Navigation Popups at the moment the live update happens, the popups window does not disappear once I move off the link. I have to reload the page to fix the problem. I have found that oddly, this is a problem in Chrome but not in IE.
I've tried with Chromium (the closest I have) and I have a persistant pop-up as well. But I manage to have it disappearing when I hover another link.
When I use Firefox, the pop-ups overlap each other when I hover a new link, but they disappear when I move my cursor.