Before going into this, haven you turned GEMDOS mode on all drives
except floppies?
Is then Kobold any good? One can use KKCommander or plain desktop I think. I don't like Kobold exactly because it does suspicious actions even on normal HDD drives, same as Jinnee -- I've got several disk crashes in my lifetime (corrupted FATs etc), as soon as I stopped using Kobold (first step) and then Jinnee (second step), I've seen none. With that Jinnee I'm 100% positive something is going wrong, I remember formatting my disk, installing FreeMiNT + Jinnee, copying some files with Jinnee's copier (IIRC it was from vfat/ext2 to normal partition) and I've seen immediately (!) some errors in Diamond Edge. And no, a HDD was good, it serves me even today reliably. Since then I haven't courage to use Jinnee again ;)