What VM program were you using? In VMWare, at least, whenever a device with a "new" USB hardware ID is plugged in, it prompts you whether it should attach it to the host or guest (and you can change this for each device at any time.)
It is (or was, don't know, this was about two years ago) a known problem: http://www.ivankuznetsov.com/2009/10/upgrading-iphone-firmwa...