Hi,
For BD25, it must have all BDMV folders like CERTIFICATE.
For BD9/BD5, it's actually AVCHD, and there are two options in "Settings -> Blu-ray to Blu-ray". If you want to play the backup with software player, you need keep CERTIFICATE, and if you want to play the backup on standalone player, you should not keep it.
I suggest to try latest 7058beta again to see the result, maybe it's a problem of old version.
Best Regards,
Fengtao