Empty window on Windows

True, but that’s not likely the problem The first is just a launcher for latest version.
That might turn out to be the originall install, or it might be some installed update.
Turning on Task Manager Image path name column can show its path locations.

which reminds me – does this weird extra window last through restarting the PC?
What’s the display setting in pixels, and can you estimate the size of the window?
The tray icon looks like it needs a small hidden window. Maybe yours didn’t hide?

Duplicati.Library.AutoUpdater.exe

explains how you can stop the second Duplicati (assuming initial install is 2.0.7.1).

You could Quit Duplicati, open a terminal window, and do manual start for testing:

set AUTOUPDATER_Duplicati_SKIP_UPDATE=true
Duplicati.GUI.TrayIcon.exe

On the topic of updates, did this show up around recent Windows Patch Tuesday?
Windows Forms is part of .NET Framework, and that tends to change sometimes.

That was the 17th, and Patch Tuesday was the 11th, but it has some grace period.
I don’t think Duplicati changed, but you could try uninstall and reinstalling as a test.
First, you should probably find your update situation, e.g. how’d you get to 2.0.7.1?

About → System info will show BaseVersionName and ServerVersionName which
are initially the same, but autoupdate will make them different as mentioned above.

and does the usual Duplicati tray icon have its usual look, unlike the odd new one?

BTW, if everything seems to work well, it probably does, but this window is strange.