Can confirm that this also happens on SharePoint Exchange - I actually created a post on meta there before finding out this is a common issue on all sites. If anyone wants to have a look the link is herehere. I will try to edit this answer if we find out something.
Anyway, I have tried to see if the IE dev toolbar reports anything worth. Just after the pop up self-closes I saw this.
Right now I can't have a look at it, so I am leaving it there for the time begin.