need to change the name in the 'atahualpa page options' and 'custom fields' areas as well
That's correct. It is an annoying new "feature." It is nice to be able to override the post title in certain contexts, but it should be an option. If you don't publish or save the post as a draft, the alternate page title won't change.
Atahualpa 3.4.6 and the few versions before it overrides the automatic smart quotes and dashes function in WordPress/TinyMCE and makes all quotes as straight quotes and all dashes as successive hyphens. Either Atahualpa should allow the automatic conversion to happen or allow the title override to be disabled.
If you make any edits to a post remember to delete the Atahualpa post title options before pressing publish or draft.