What happened when you got into a flagging war with another user? As I was researching a post about the reputation calculation I found that any flagging war is certain to be won by the party that has the superior reputation. For example, if you flag this comment (please don't) it will have a negative effect in proportion to your voting power. If I tried to retaliate by flagging all of your active posts and it would have no effect on your reputation, but it would drain my voting power. If we kept it up long enough my reputation would drop below 25 and then I wouldn't have the ability to change anyone's reputation, up or down. The user with the higher reputation is guaranteed to win as long as the war is one-on-one.
If you find any claim in the post that I linked above, please let me know while I have time to fix it.