This happened to me when i deleted all my Bioshock info from my system after getting a few of the early trophies. After i re-installed it would always give me the 'toaster in the tub' trophy and when i would check the list it would say it was the only trophy i had. Although after re-syncing with the server it would always correct my list to what it should have been.
If you synced your HR trophies with the server they should be safe, if not I'd try and get one of the easier trophies to see if you can 're-earn' them or if they have glitched.
Should just be a case of re-syncing your list with the server though?
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