I've been in contact with Amazon CS about this issue and directed the, to this thread. Today I got this email
"We apologise for the problem you have experienced with Send to Kindle for PC. Just to let you know, we have released a new version of this application that should fix the problem for you.
To get the new version of this application, click on the following link to start the download:
http://s3.amazonaws.com/sendtokindle...ler-v1.0.1.237. After the application has downloaded, open it to begin the installation."
I don't need to test it as I've loaded the updated roots manually, but I thought I would mention it here.