Quite a lot of effort has gone into improving this behaviour in the
development branch of GIMP. We tried to make most, if not all, popup
windows transient to their parent window. This improves usability a lot
and it reduces clutter in the taskbar.

Unfortunately though it turned out that this doesn't work on the Windows
platform. It doesn't seem to be possible to make dialogs that are
created from a plug-in transient for the image window as that window
belongs to a different process. Windows users will thus not benefit from
a lot of the usability improvements that have gone into the 2.3 series.


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