Have the same problem on lubuntu 12.04 LTS and gnupg 1.4.11-3ubuntu2.6.
It seems like the symlink create a problem like partition was fat 
http://lists.gnupg.org/pipermail/gnupg-users/2005-January/024236.html

If I add lock-never option, got another problem:
gpg: fatal: /home/user/.gnupg/trustdb.gpg : base de confiance incorrecte
secmem usage: 0/0 bytes in 0/0 blocks of pool 0/32768

If I reverse and do a real dir file and symlink my
gpg.conf/pubring/secring/pem, it works normally

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https://bugs.launchpad.net/bugs/943940

Title:
  Can't generate a new key if the .gnupg dir is a link to a dir in
  another partition

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