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Have you tried removing Calibre from the equation and just transfering the books direct from ADE to the ereader? AFAIK uninstalling and re-installing Calibre doesn't reset its configuration.
Calibre is able to transfer purchased DRM books (without removing the DRM), but I don't think it can transfer borrowed books (without removing the DRM), perhaps because the borrowed books need some sort of interaction between ADE and the ereader to set the expiry date.
If you had one version of Calibre set up with plugins to strip DRM and the other not, then that could explain why one was able to transfer borrowed books and the other couldn't.
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