This question already has an answer here:
W.K.T, when a user got a downvote for his posts before getting any reputations will not get any negative reputations.
So, after getting positive reputations, the user should get his penalty(-2) since his/her reputations can get substracted to get a positive number.
But, it doesn't happen like that in SO. for ex, take this question, it got 3 downvotes and 3 upvotes and see the user's reputations.
Is this an issue or the fact of SO.