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The problem there is that then if I disconnect it, it sounds like I am causing errors. I know it is SUPPOSED to automount in ubuntu.
No, but what will happen is that ubuntu is not mounting it (or in some cases it is in the media folder under a name like "sda2") but the ipod itself says it is connected. Therefore, there is no way to safely disconnect it (and I mean physically disconnect it).
eject /dev/sda
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