Linux seems to have weird USB power saving features, my Kindle 3 only gets some charge before Linux powers down the USB port.
When the device is mounted, it doesn't get enough power, with this same hardware under Windows I don't get the message on the Kindle "currently your kindle is not charging." When I eject the device it gets no power at all. I've had a bit of a look around in /proc
That is strange indeed, for I've been hunting for a way to turn off power for USB ports in Linux and comprehensively told that Linux won't do this, at all, ever.
You could try disabling USB power management in your kernel.