Happens to me at least 4 out of 5 times.
Ubuntu 17.04
System76 Meerkat
Using the following always make the updated visible on my current desktop:
wmctrl -R 'Software Updater'
I can collect data if there are questions since it happens so often.
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https://bugs.launchpad.net/bugs/1671540
Title:
Software Updater window is invisible
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