I had this problem, and as you have probably found yourself, if you keep trying it eventually works. By 'works', I mean that you get to a window showing the partitions on the disc, but stating that the Bootcamp partition is not correctly formatted (NTFS). On my system (MacOS LIon) this is dealt with by the Bootcamp documentation, and you click on a link to get the option to format the partition ... and then it is (relatively) plain sailing.
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