Select single window while in remote desktop

So I am using the feature which allows me to select a single application window on a remote desktop. The solution works perfectly for a single connection. When I make a second connection to the same computer (to view a separate application) the application only view is escaped and goes to full desktop for both the old connection and the new one. If I then try and select a single application with both connections active, both connections freeze and I have to close and reconnect.

Is this expected behavior?

Thank you for your help,

Chris