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I have come to the concusion the reason Neg Rep caused problems:
It was Yoda's fault.
He didn't establish guidelines for using neg rep. This is how some bodybuilding forum (which I will never visit again because I dont have anything in common with those people) describes the proper use of neg rep:
Negative reputation should be given if the person is posting something that detracts from the conversation. If the post is rude, inappropriate, breaks forum rules, is not gracious, etc; these are all good reasons to give negative reputation. If you have a personal grudge with someone, their team, etc, is it not appropriate to give them negative reputation for no reason. Giving negative reputation because you don't agree with what was said is not an appropraite use of the reputation system. People are entitled to their own opinions, and just because you don't agree doesn't mean the user was wrong or not contributing to the conversation.
That is pretty much how I was using it. If the guidelines for it was made clear, and moderators reiterated it in situations where it got tense, it wouldn't have created the problems it did.