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В общем, такая вот ошибка, как возможно её решить без переименования 
исходных файлов?
mkisofs: Error: 
./ubuntu_amd64/ubuntu1/pool/main/x/xserver-xorg-video-ati/xserver-xorg-video-radeon-dbg_6.9.0+git20081003.f9826a56-0ubuntu2_amd64.deb 
and 
./ubuntu_amd64/ubuntu1/pool/main/x/xserver-xorg-video-ati/xserver-xorg-video-radeon-dbg_6.9.0+git20081003.f9826a56-0ubuntu2.1_amd64.deb 
have the same Joliet name
mkisofs: Joliet tree sort failed.