I don't think 1.3.36506-0ubuntu2 really fixes the bug:

  $ dpkg -l|grep ec2-api-tools
  ii  ec2-api-tools                                           
1.3.36506-0ubuntu2                        Amazon EC2 API tools
  $ dpkg -L ec2-api-tools|grep \\.cmd$|head -5
  /usr/bin/ec2assocaddr.cmd
  /usr/bin/ec2-migrate-image.cmd
  /usr/bin/ec2daddr.cmd
  /usr/bin/ec2gpass.cmd
  /usr/bin/ec2-purchase-reserved-instances-offering.cmd

The problem appears to be that the install/ec2-api-tools rule in debian/rules 
is run before dh_install.
CDBS provides binary-post-install/* rule for doing stuff after dh_install and 
friends, and using that
seems to work (see the attached patch).

** Attachment added: "Use binary-post-install/ec2-api-tools instead of 
install/ec2-api-tools"
   http://launchpadlibrarian.net/29681435/ec2-api-tools.patch

-- 
Please remove the .cmd files in bin
https://bugs.launchpad.net/bugs/363931
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