I have a project here which is showing this behaviour.
I am using hugin_executor branch (6771:7a2a12e71e67) built on Fedora 20 x86_64.
The source images are two uncompressed tiff (~70MB each) and attempts to 
downsize them to provide an acceptable attachment size and still exhibit the 
problem have been unsuccessful. These are 16 bit tiff.
Attached archive.zip includes project 0007-0008.pto, exiftool output for each 
image (0007exiftool.txt, 0008exiftool.txt) and a screenshot (Selection_002.jpg).
The screenshot shows the two images (lower right) the Fast Panorama preview 
(upper right) with cropped pano. The image in lower centre ((0007 - 0008.jpg) 
shows the resulting stitch.
I am using enblend 4.2, which describes itself as enblend 4.2-3270515e2517.
If I can get some reasonable sized images that show this problem I will provide 
them.

Cheers,
Terry
 


** Attachment added: "archive.zip"
   
https://bugs.launchpad.net/hugin/+bug/1405035/+attachment/4286809/+files/archive.zip

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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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