Have you tried "side loading"? Plug your Kindle into your computer with the USB cable and open up the Kindle directory in a new window. Open the folder where your ebook file is stored (might be stored under My Documents, or the Kindle for PC file folder, or perhaps Calibre). Copy/paste the file into the Kindle directory folder.
Also, do you have Kindle for PC and the new Kindle registered to the same account? If not, that might explain why things are not syncing properly. Does Calibre give you any kind of error message when you try emailing to the Kindle? Double check that you have the correct address and that if you're using the @free.kindle.com address, you're connecting to wifi instead of 3G to download.
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