This doesn't seem to be restricted to QF only. Last year, Mrs AN*G and Master 5 were on the same PNR, on an LH flight (business), between FCO-FRA. Both are Star Alliance Gold.

That flight was lightly loaded, and the LH algorithm kicked in to block an empty seat next to each Gold FF. You guessed it - the system wouldn't check them in seated next to each other, since the seat next to each was "blocked". Apparently took a couple of phone calls to a supervisor to release the blocking.