The Emote problem happens consistently even when I have only one project open, which is almost always the case.

I rarely have multiple Cubase projects open at one time. 

To clarify, do you run into this issue when you first open Cubase and load your first project with an instance of Emote in it, or is it only when you load subsequent projects?

Also, when you say that Emote fails to connect, does it attempt to connect and fail (you should see a blue "e" symbol, and a dialog box when Emote eventually fails to connect)? Or is the button to connect greyed out and not working?