I asked around and this is an overly verbose sbsigntool which should probably 
not a warning but a debug message:
https://twitter.com/mjg59/status/689745355202691073

** Package changed: linux-signed (Ubuntu) => sbsigntool (Ubuntu)

** Summary changed:

- Setting up linux-signed-image-3.8.0-21-generic (3.8.0-21.32) ... warning: 
file-aligned section .text extends beyond end of file
+ sbsigntool warning: file-aligned section .text extends beyond end of file; 
checksum areas are greater than image size. Invalid section table?

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https://bugs.launchpad.net/bugs/1180649

Title:
  sbsigntool warning: file-aligned section .text extends beyond end of
  file; checksum areas are greater than image size. Invalid section
  table?

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