Same experience on BRU-FRA then FRA-GVA, however it took 3 check-in agents 15' to check my luckage through.
However since I arrived just 35' prior departure they were not waiting for me nor could I checkin any more cia LH.com, and had to get from Terminal B to A.
Therefore I would advise to checkin electronically since your less then 24 h from departure and this way you are expected in case of delayed arrival.