I don't usually use Calibre inside my VM (Windows 7 guest; Kubuntu 14.04 host), but I just tried it with my Kindle PW1 (sorry, I don't have a PW2) and it worked fine. I'm not sure what you mean by the "USB filter," but in my case I had to select the dropdown menu Devices > USB Devices and then check the box next to "Amazon Kindle." It took a couple of minutes for Calibre to recognize that the Kindle was attached and another couple of minutes to generate a list of titles on the device (much longer than when I run Calibre in Kubuntu), but still it worked.
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