Question: The Update Manager recently started itself and found two updates. I can tell by the icon in the launcher. The icon has a (2) on it and a little white arrow saying the application is running. I can also see the update-manager process in a 'ps -A' list. Alt-Tab also shows the Update Manager.

The problem is I can't get Update Manager to show up. If I click on the icon or Alt-Tab to it, nothing happens. I've never had any issues starting it manually, but when it starts on it's own after finding an update, I can't switch to it.

What can I try to make this work better?

Answer: 
I have the same problem. I didn't find this specific issue on launchpad either. For me, even though the update manager doesn't completely open, it still can be closed from the "x" on the top right panel or ctrl+q. Once closed it reopens fine.
I have this problem with libreoffice.

You can use 'super + w'. You will get all the window on screen, click the window you want.