I was able to reproduce your results but there aren't that many patches
being applied at the moment and that makes the failure surprising. I
didn't spot anything obvious in the certificates either but overall I
think this bug needs a reproducer which covers the generation of the
certificates because this is a very common worfklow and I'd be surprised
it was completely broken without many people noticing.

** Changed in: openssl (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1441461

Title:
  openssl verify fails with "certificate signature failure"

Status in openssl package in Ubuntu:
  Incomplete

Bug description:
  I have a intermediate certificate signed by my own CA, which works fine on 
other systems.
  but openssl (1.0.1f-1ubuntu2.11) installed with apt-get will always fails 
with "certificate signature failure"

  but openssl binary compiled myself with the same version of code
  (1.0.1f), works.

  so i wonder if this is a bug of openssl?

  certificate details and version info is at
  https://gist.github.com/bearice/e2dd5d4245472e1b3992

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