Thanks for the pointers, but… I’ve analyzed the audio and removed the silent channels and I still have this problem.
Creating a multi-cam clip does work though, but I really thought that I would not need to go there, it seemed “wrong” to me.
I’m not sure whether the channel configuration has something to do with it. The video clip is obviously a stereo (with the guide tracks), but the externally recorded audio tracks are three separate mono channels.
I did a search on the Apple support forums, and I found an identical problem with someone having the identical setup as me – stereo guide tracks on the video and 3 mono channels.
This is such a stock standard configuration, I’m scratching my head as to why this is not working.