Since I just started using Raptr, this issue is annoying as hell! Since Sony apparently doesn't allow any sort of "data stream" or API for trophy and game info, this horrible website is the only place Raptr can pull game and trophy data from.
My true trophy count: 1395
My Raptr trophy count: 848
Missing a ridiculous 547 trophies!
post under helps section on raptr with a link to your playstation profile and one of the staff on raptr should be able to fix that for you.
Has anyone found a solution to this? I've only earned trophies for three PS3 games (Batman Arkham Asylum, Batman Arkham City and Final Fantasy 13) but for some reason, PSN leaves out listing Batman Arkham City. PSN definitely counts the trophies I've earned on Arkham City but it doesn't show it as a title I can drill down into and see my progress.
My list is missing some games as well. I have asked @AskPlaystation and they forwarded it on the the "Web Team". I still haven't received an answer.
Not sure what else to do.
UPDATE - I am seeing all of my trophies now. Apparenly they made some change somewhere. Not sure what they did but it worked.