Comment 6 for bug 814496

> So the problem seems to be that if hugin is in the foreground and
> PTBatcherGUI is in the background, the dialog is hidden by hugin's
> window. Maybe bringing the batch stitcher to the foreground when
> it receives a job and immediate stitching is activated would mend
> the problem.

This sound easy. But this is not supported by all (?) window managers. An inactive window can not automatically bring into the foreground by the program itself. This is done only by the window manager.

So the exact behaviour of the window manager seems to be responsible how the windows react.