I’ve had that happen before, but it was with version 5.04…don’t know what i did, but there’s two things I can think to try.
1. Open FCP by double clicking a project file, rather than open via the application menu or taskbar. This kind gives what I’d call a ‘soft’ preferences reset. When you open FCP via application menu, it opens all the projects you had open the last time it ran, holding onto any extraneous data. Opening just a project file does just that, and nothing else.
2. at the top of the batch capture window when it first comes up, the one that asks what format you want to capture everything with….The top drop box should read “capture selected items”. If you get a dialogue saying along the lines as there’s other associated media, do you want to capture it, say no.