This is due to an issue with the new Contact Select Record Type (cv__Contact_Select_Record_Type) VisualForce page that was added in version 12.11. 

To resolve this behavior, change the override on the New Contact button so that the old VisualForce page is used instead.  Here are the steps to do so:
1.  Navigate to Setup > Customize > Contacts > Buttons, Links and Actions
2.  Look for the button with a label of "New" and the name of "NewContact".
3.  Click Edit next to the button name.
4.  In the Override with section, select "Contact Dupe Check [cv__Contact_Dupe_Check]".
5.  Click Save.

New Contacts created from an existing Account will now be associated with that Account.