Yep, that soughted it.
I deleted one board from the sketch and then exported as pdf, all worked fine.
It apparently doesn't like 2 boards in the same sketch even though it prompts you to select one of the boards for export. (linux maintains it's innocence:-)
I guess I'll have to split the circuit into 2 sketches.
I think this is still a bug though.
Thanks old_Grey.