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Since June 3 my reputation for "IT Security" is showing different values in SE reputation graph and everywhere else. This happened just after an user were removed, making me lose all reputation from his upvotes and my answer/edit to one of his questions (I'd link to it, but I don't have enough rep to even find it again). I waited a while to see if recalc would fix it, but so far nothing's changed (before asking this, I also manually triggered recalc, but the values are still the same).

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It seems when this user was deleted, all reputation changes coming from him were removed from the history, since there's no "drop" in the graph that day I lost 67 points. My first guess were that -10 User was removed was the culprit (since the discrepancy is also 10 points), however the graph is the lower one...

Another explanation would be: since that user [likely] upvoted my answer to his own question, when he was deleted the history removed his upvote twice: once because "he upvoted me", and another because "I had X upvotes in an answer that was deleted".

Update: I understand it might be a caching problem, that's why I waited almost 3 weeks to report. However, note that until June 3 both the graph and the site were in sync, and after that they still are in sync, but with a discrepancy of 10:

Date              Graph                    Site
         before del | after del  before del | after del
June 1         1038   971              1038   971
June 2         1043   976              1043   976
June 3                966                     976        (-77 | -67)?
June 4                986                     996
June 5                996                    1006
June 19              1056                    1066
June 20              1066                    1076
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marked as duplicate by hims056, Lucifer, Oded Jun 22 '13 at 6:51

This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.

I don't think it's a caching problem - the discrepancy appeared at the same day an user was deleted, and has been pretty consistent for almost 3 weeks. Please check the update – mgibsonbr Jun 22 '13 at 6:37