They should be adding Trader ratings back, so keep the information. Right now if you have an x with a check under the other person's name you can add to their reputation. Most of us do not and can't leave reputation points. As soon as they create an updated version of Trader Rating for vbulletin 3.5 it will be updated here.
It works for me I've added some rep to you guys, anyone knows where you can see the rep comments in the User CP? Seems to be missing in mine, maybe nobody gave me any rep :-D
Yeah, the rep system is very strange, I don't think the trader rating points have anything to do with your rep though, someone must have given you bad rep.