Hi Ben,
For BSE simulation, you should use CASINO v3 and not version 2. Also you need to specify which elastic cross section models you use. In CASINO v3, from a limited testing, I found Mott-Browning model to closer match with the Joy database, but the ELSEPA model should be better. PENELOPE use ELSEPA, but I am not sure which settings they have use to generate the cross section, so it may explain the difference between CASINO ELSEPA and PENELOPE ELSEPA.
Regards,
Hendrix