Try to make separate bins within your Project window rather than just having the Project window be the “Logging Bin”. In other words, make a new bin for your footage within the project window, make that new bin your Logging Bin and batch capture from that bin. That should eliminate FCP from wanting to capture everything in your entire project window.
Also, Quit your project(s) BEFORE Quitting FCP to stop it from opening up the last project(s) you were working on when you launch the application. I always launch FCP from the Project itself and rarely by just launching FCP by itself.
Tom