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[tmodes <1405039@xxxxxxxxxxxxxxxxxx>]

Concerning the 2 other windows: One is the verbose output, which you have activated. This one can be easily deactivated in PTBatcherGUI:
The second one is connected with the GPU remapping. It is shown by the freeglut library, not by Hugin.
I have not found a way to deactivate the window in freeglut. (On Windows I'm getting the window only with the freeglut lib, not when using the glut lib.)
Maybe you found a solution and then I will apply the patch.
But the cleanest way would be to fix the issue in freeglut.

** Changed in: hugin
       Status: New => Won't Fix

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https://bugs.launchpad.net/bugs/1405039

Title:
  Should be possible to work in only one window

Status in Hugin - Panorama Tools GUI:
  Won't Fix

Bug description:
  Saving a remapped image results in 4 (!) windows being opened:
  http://i.imgur.com/51u28rp.png
  The main Hugin window, the Batch Processor window, and two other windows. One of them, the one in the top-left corner, appears for a few seconds with no meaningful content, and then disappears. It seems to do that for every source image in the pano.

  In addition to the obvious, this is a pain in the ass because all
  these windows flashing on and off mean I can't work on something else
  while Hugin renders because I keep being interrupted and focus keeps
  being stolen.

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