Here is some more info which may help to decipher the problem.
I've since discovered that the objects which turn Blue are in fact References of References. What on Earth does this mean?
Well the scene snapshot I've attached above is Referencing a Study scene and a character. HOWEVER the study itself is referencing the file with the desk in it. So in effect that blue desk's actual file is two reference jumps away.
Am I getting closer to the problem?
Maybe if I'm still none-the-wiser in a few days I'll post the scene files but for now I'm happy with suggestions
Thanks
Barry