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RE: Seagate GoFlex Home server causes setup.exe build to fail, "cannot run /bin/sh cfgaux/config.sub"
Officially, I don't think there's a way to modify the file system. It's designed to be an appliance. I've contacted Seagate support to see what they say.
That said, I've just found out how to get SSH access into the server and am poking around now. I downloaded their GPL source earlier and found Samba 3.0.28 included. Running "ps" on the box shows it is running smbd. I'm hoping there might be some way to modify their smb.conf to turn on FAT file attributes.