New Identity fails to close windows with prompt dialogs

Steps to reproduce:

1. open a new tab
2. press CTRL+SHIFT+K to open the console
3. type alert(0) in the command line and press enter
4. press CTRL+SHIFT+K to close the console
5. select New Identity from Torbutton

The tab will fail to close. I noticed this on a website that prompts users when it detects a Tor exit node, if you press New Identity without closing the alert dialog then the tab will remain open.