Ludwigs test with 2.0.9 + patch shows that the error message does
not come anymore.
Werner, can you state when you did the change the dirmngr?
(E.g. what is the last released version that worked correclty here?)

Tested with gnupg2 2.0.9-1 from Debian sid and python-pyme 0.7.0-4.

Related to the certificate duplication is the new
issue876(CMS certificate duplication blocks use of gpgme_get_key() )
so all symptoms are not remedied in gpgme 1.1.6 and gnupg 2.0.8 yet.

Volker Dormeyer reports that the problem is also there with
gpg --version

gpg (GnuPG) 1.4.6    
[..]

Note if you want to check if you message has this problem,
try gpg2 on the command line like

Werner,
thanks for the fix.
Just quickly?
In which component did you fix it? Is there an easy way to get a patch?

It used to work in earlier versions and this issue
now block rollout to production customers, thus a warrenty kks
and "urgent" because of the blocking effect.

$ locale
LANG=de_DE@euro
LANGUAGE=de_DE:de:en_GB:en
LC_CTYPE="de_DE@euro"
LC_NUMERIC="de_DE@euro"
LC_TIME="de_DE@euro"
LC_COLLATE="de_DE@euro"
LC_MONETARY="de_DE@euro"
LC_MESSAGES="de_DE@euro"
LC_PAPER="de_DE@euro"
LC_NAME="de_DE@euro"
LC_ADDRESS="de_DE@euro"
LC_TELEPHONE="de_DE@euro"
LC_MEASUREMENT="de_DE@euro"
LC_IDENTIFICATION="de_DE@euro"
LC_ALL=

Using the patch svn diff -r 4567:4568
my gpgsm can do encryption again.
Still the duplication stays in the keybox.

(updated version number and assigned to werner, if this is okay)