For your first question, go to Tools > Options > System Options > External References. In the Assemblies section, check the box for "Update component names when documents are replaced". I can't imagine why anyone wouldn't want them updated, so I don't know why this is even an option, but that should fix it for you.
Thanks for that! I'm not quite sure how the checkbox flip-flopped in our settings when we upgraded but who is ever sure why solidworks does some of the things it does. I agree with you though, I'm not sure why this is even an option who would want to have the wrong part name displayed in their design tree ever???