I've tried to reproduce this as well and couldn't either.
I started with a Xenial VM that had an older version of gnupg2 than 2.1 installed.
I generated a key, and verified I could see it with both gpg and gpg2 as well as in seahorse.
I then upgraded to gnupg2 2.1 and checked with gpg2 --list-secret-keys and the import process worked properly.
thanks for your comments daniel.
I've tried to reproduce this as well and couldn't either.
I started with a Xenial VM that had an older version of gnupg2 than 2.1 installed.
I generated a key, and verified I could see it with both gpg and gpg2 as well as in seahorse.
I then upgraded to gnupg2 2.1 and checked with gpg2 --list-secret-keys and the import process worked properly.