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[tmodes <1405035@xxxxxxxxxxxxxxxxxx>]

Enblend does combine 3 images:
enblend: images do not overlap - they will be combined without blending
..
enblend: images do not overlap - they will be combined without blending

Without the pto file it is impossible to find the cause.
What also look suspicious are the warnings in the files. There are many duplicate tags in the TIFF files which Hugin uses. This should be fixed before. Which software have touched these images and produced these duplicate tags? I never seen this by Hugin.

** Changed in: hugin
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1405035

Title:
  Saved TIFF contains only one of the source images

Status in Hugin - Panorama Tools GUI:
  Incomplete

Bug description:
  Using 2014.1.0.9b4acbc72451 (today's head, 2014-12-23), when I save a TIFF which consists of a 360x180 equirectangular layer and two 90 degree rectilinear layers (nadir and zenith), the saved TIFF contains only the zenith.
  Photos tab:
  http://i.imgur.com/8iMlqZE.png
  http://i.imgur.com/4cXra2I.png
  http://i.imgur.com/aVD9TEL.png
  http://i.imgur.com/SUc6end.png
  http://i.imgur.com/3WLRITR.png
  Fixed EV http://i.imgur.com/7h4s7Bu.png
  Fast panorama preview shows the correct pano which includes all layers http://i.imgur.com/TbV5FIz.jpg
  Stitcher tab http://i.imgur.com/MLujWqe.png
  Saved TIFF (after fixing the alpha bug 1405025) http://i.imgur.com/xyYjixV.png

  Log file attached.

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