Hugin is using absolute ev values in the exr files. Therefore clipping can 
occur, when the value range of the exr file is overrun (as already found out).
A possible solution is the use relative ev values in the exr files (Implemented 
in changeset 7b8ada736647). This changes the behaviour when outputting exr 
files. Now the output exposure value has an influence on the exr files and 
needs to be set to a middle exposure also for exr output (when setting the 
output exposure value to zero, the old behaviour is retained). I hope that this 
fixes the overflow and the final output has no more black areas. 
Please test, if this does not break other side of the exr output and report 
back. Thanks.

** Changed in: hugin
       Status: Confirmed => Fix Committed

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https://bugs.launchpad.net/bugs/678694

Title:
  EXR files quietly clipped (black rectangles in output)

Status in Hugin - Panorama Tools GUI:
  Fix Committed

Bug description:
  The EXR file format has a maximum encoding value of 65504.   The Hugin
  data flow maintains the absolute exposure through use of the Ev field
  which effectively scales pixel values.   When using Hugin/Nona on an
  HDR series that includes very bright elements (such as a very bright
  sky with a very short exposure), some pixels end up with values above
  65504.   When these are written out by Nona, those pixels are written
  as NaN's in the EXR output file.

  If enblend is then used, the problem is further exacerbated.   A
  single NaN pixel results in NaN for entire rectangle of enblend's
  pyramids.   The end result are large black rectangles in the output
  file.

  If output is changed to TIFF, then everything works fine.

  Nona should warn when clipping occurs and then output the maximum
  possible value rather than a NaN.   I assume this is the OpenEXR
  library itself and probably affects other applications.   In fact, if
  a TIFF generated as above is opened in PhotoShop, it looks fine, but
  if it is resaved as EXR, the same NaN pixels are created.

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