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I suggest you continue to use it that way then. Don't use the eject functionality in calibre.
On linux setting up automounting is often difficult for users, so I've decided to provide this facility in calibre (it should really be handled at the OS, not the application level). Because of the large variability on existing automount solutions/kernels, it's very hard to come up with a system that will work for everybody, so if you have a system that works, stick to it.
EDIT: I should also say that whatever automounting system you're using is broken if it is not creating entries in mtab
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