Recently installed updates that required a restart. At the end, I was presented two buttons: "Close" and "Restart" -- I clicked "Close", only to be presented with another dialog which I believe just had another "Close" button.
I attempted to confirm the exact text of these dialogs, for the purpose of this bug report, in VirtualBox, but alas, when I got to the first dialog (with "Close" / "Restart"), I went back to my system to read an e-mail that just came in ... when I went back to VirtualBox, the PackageKit window had disappeared entirely, though I had not selected any option. The restart icon was in the notification-area though. I guess I should file another bug report? Are you getting sick of hearing from me yet? :-D
Known bug, I'll be fixing in master when we land the glib2 stuff.
This is probably related --
If the user instead clicks "Restart," the second dialog still comes up saying "all updates have been installed" but immediately closes, obviously, because the system is rebooting. This is just slightly disorienting and redundant, since the user has already made the decision and obviously is aware that the update is complete.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.