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[tmodes <1049904@xxxxxxxxxxxxxxxxxx>]

Confirmed. 
The issue is that the mask is handled as a list of points. When the mask contains the nadir or zenith and the mask expands over the +-180 border the mask is incorrectly transformed.
I tried some approaches to fix it. But until now I have no solution which works for all use cases.

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

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https://bugs.launchpad.net/bugs/1049904

Title:
  Wrong 'Include region' mask appliance to equirectangular/cylindrical
  image

Status in Hugin - Panorama Tools GUI:
  Confirmed

Bug description:
  I noticed this bug when tried to fix nadir/zenith errors by blending already stitched 360x180 panorama and retouched patch. Instead of applying 'Exclude region' mask to the pano I applied 'Include region' to the patch (which is simpler due to equirectangular distortion of poles) and get completely wrong exclusion on other image (look "0 - initial occurrence.pto").
  First I thought it is related with poles on output projection, but after playing with shape of the mask, FoV of images and projections I found that it is not entirely the case. And occurs only on equirectangular/cylindrical projection of input files - other projections are ok.

  I think it maybe somehow connected with transition through right/left
  borders of equirectangular/cylindrical input image, maybe poles
  somehow involved too, but I'm not sure. After playing with different
  parameters I failed to define clear reason why it happens. Moreover I
  found a case when images intersect but mask in one image do not cover
  another at all but causes error ("3 - weird case.pto"), this I cannot
  explain at all.

  I have attached ZIP archive with pto files, images and screenshots to
  show what I'm talking about.

  --------

  Operating System: Windows NT 6.1 (build 7600)
  Architecture: 64 bit
  Free memory: 7279636 kiB
  Active Codepage: 1251 (Cyrillic Windows)

  Hugin
  Version: 2011.4.0.cf9be9344356 built by Matthew Petroff
  Path to resources: C:\Programs\Hugin/share/hugin/xrc/
  Path to data: C:\Programs\Hugin/share/hugin/data/

  Libraries
  wxWidgets: 2.8.11.0
  libpano13: 2.9.18
  Boost: 1.44.0
  Exiv2: 0.20.0

  --------

  Operating System: Windows XP (build 2600, Service Pack 3)
  Architecture: 32 bit
  Free memory: 2097151 kiB
  Active Codepage: 1251 (Cyrillic Windows)

  Hugin
  Version: 2011.4.0.cf9be9344356 built by Matthew Petroff
  Path to resources: C:\Programs\Hugin/share/hugin/xrc/
  Path to data: C:\Programs\Hugin/share/hugin/data/

  Libraries
  wxWidgets: 2.9.2.0
  libpano13: 2.9.18
  Boost: 1.46.1
  Exiv2: 0.21.1

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