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It's highly unlikely that it's your phone, as its integration on HTCSense.com is nothing more than a link via the web. Have you tried deleting your HTCSense account, and then recreating it from the phone & not via the web?
HTCSense thinks my old Desire is an HD, what with the HD ROM and whatnot. It works fine here at present, but it's been a biatch to get working - with numerous deletions and recreations - after a couple of ROM flashes in the past.
One of my biggest gripes is it keeps stuffing up my contacts.