Are you doing that in a virtual machine? After uploading the RAM kernel, the Kindle is triggered to run it. In that very moment the USB connection is reset and comes up a tad bit differently. I always have to manually enable USB forwarding for that "new" device in the virtual machine (I'm using WinXP in a VirtualBox instance running on a Linux host).
PS: Also, I'm almost through a rewrite of the flashing capability using libusb. Should be 1-2 days until I have that running, will publish the code soon.
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