I have seen this happen in two different cases:
1) The file that was added has since been deleted. Sometimes a bogus file is added and a mod removes it.
2) I go back to that page (browser history), and it gets the trigger from when I first opened that page and since it had shown me the notification the first time around there are no new notifications to show.
Whatever the case is, you can alway go to mynotifies (from myplaces) and click on the show history (at the bottom of the page) and it will show you what notifies there were.
another cause can be "webaccelerators", basically software which preloads html pages in the background. If that leads to a situation where the popup is loaded twice, it will be empty.