If an old installation of GnuPG exists which is not from GPG Suite, GPG Suite will install our version of GnuPG along side the old installation.
This leads to issues however, if the old installation is GnuPG 1.x
In order to remove the old installation please run the following commands in Terminal.app:
sudo rm /usr/local/bin/gpg
sudo ln -s /usr/local/MacGPG2/bin/gpg2 /usr/local/bin/gpg