Here is a nice explanation and how to fix the problem: LinuxQuestions.org- The iPod and the Penguin – LinuxAnswers

At the end, I enabled additional partiotion types and disabled the EFI. It seems to work now. CONFIG_PARTITION_ADVANCED=y CONFIG_MAC_PARTITION=y CONFIG_MSDOS_PARTITION=y

CONFIG_EFI_PARTITION is not set

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