I have noticed that LH would only check me in as far as BRU, i.e. before the FlyBE segment. I tried accessing my booking via the FlyBE website but it wouldn't recognise the booking code.

However, I was able to access it via the Brussels Airlines site, and seem to have been able to choose a seat as it has issued me with a boarding pass specifying my choice. The LH site still shows the default seat they kept resetting me to, however. Let's see what happens - will report back for others for future reference.