[demoric]

I use my Kindle in Ubuntu linux, and I have always had to disconnect the kindle from USB to be able to use the device to read or to test modifications.

In Windows if you eject the kindle it still charges over usb and allows you to use the device as a kindle. However in many linux distros the option you are shown in your GUI (Ubuntu's is Nautilus) is to un-mount the device which does not permit you to use the device to do anything while charging. If you want to still be able to read your kindle or use it's other features you have to use the eject command instead of unmount.

sudo eject /dev/sdb1

Please note: the device location may be different on your system to find the device open a teminal window and type: sudo fdisk -l and search for a device that uses a W95 FAT32 filesystem change the /dev pathway as needed. Also, some distros will not need the sudo aspect of the commmand line.