I noticed that too, sometimes it works as expected when Ubuntu boots up,
but then Nautilus gets an error and that's when the bug starts.
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https://bugs.launchpad.net/bug
Public bug reported:
When 'Files' has one window open and is in the background, clicking on
'Files' to bring the open window in front, opens a new window instead,
then by right clicking on 'Files' can the open window be selected. Even
with the Files window open and in front, clicking on Files open
