I had the same problem. I ignored the error message and selected the 'print boarding pass' option. There is no mention of my FFP but the boarding pass includes an invitation to the lounge, so clearly my Sapphire status is there are recognised by the system but there is no proof of it on the BP.

I will just go ahead with this and get them to print the BP at the airport and ensuring my BAEC is reflected.

Lousy system.