To take this noisy answer as an example, flagging spam doesn't give the total vote count a -1 anymore, but when I open the vote count, it is there. Until about a week ago this has worked fine.
Update: it seems that they get fixed by some daily script.
Although this all get fixed by some daily script, this hasn't occurred until a few weeks ago. So I'd say, there has been a new bug introduced meantime which needs to be fixed.
Update 2: The same problem by the way occurs when serial downvotes get removed by the downvote anomaly checker script. The total vote count still remains the same, but when you open the vote count, it's correct.
Update 3: They are now also not anymore in the vote count details (when you click the vote count total). Until about a week ago this was the case.
So, something has changed?