I use gpg key on a Yubikey Neo and this works correctly in Trusty,
Utopic and Vivid.

Make sure that in startup applications "GPG Password Agent, GNOME Keyring: GPG 
Agent" is unchecked.
Clear custom changes to bashrc.
Logout, login.

Check that gpg-agent upstart user session job is running (In terminal, $
status gpg-agent)

Check environment is pointing at gpg agent, rather than anything else
(e.g. gnome-keyring etc) ( $ env | grep gpg )

** Changed in: gnome-keyring (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1387747

Title:
  No longer asks for passphrase, no access to private key

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