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I have both a mac and a linux system, and I connect my kobo to both.
While I haven't had any huge problems per se caused by kobo's interaction with these two systems and calibre, I can say for sure that there is something wrong with the way kobo handles the usb interface.
When I plug the kobo into either system, it is recognized as two devices -- one is the kobo internal disk, the other is my SD card plugged into the kobo. Both of these show up, and as separate disk devices.
If I eject *either* of these two devices, both devices are disconnected, as if the USB cable had been suddenly pulled. It doesn't matter if I had files open on the one not being ejected, it gets removed without the filesystem being properly unmounted.
Once I noticed that, I made sure that if I am manually ejecting the device, I unmount the filesystem on the other device before ejecting. (Ejecting in linux and mac automatically unmount the device being ejected.)
I have other devices (including an android tablet) that show up like this as two disks (for the same reason), and none of them disconnect both disks when one disk is ejected.
For some reason, when calibre is told to eject the device, it doesn't typically cause problems. Maybe because there are no files open on either filesystem when it does it, maybe because it issues eject commands to both devices fast enough that they get ejected properly at the same time. Maybe calibre issues unmount requests before it ejects. Maybe I've just been lucky. I don't know. But the way kobo handles this is certainly wrong.
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