midnight_Sun323, firstly try not to upset the people who are actually here to help you try to work through your problems, these are all good commanders and have helped many people in the past.. Myself included

I think you just got the wrong end of the stick which is easily done on forums

no harm done anyway but it had to be said
What they are trying to say is that as you say in your Opening post you used the "KWS" scanner to track these prates down, that's probably the reason your getting negative rep. I will explain why.. Even though the patch notes say wanted status ships wont effect your reputation, what they Actually mean is wanted status ships that are wanted in the current system, you are playing in wont cause you negative rep

..
You see the "KWS" will look for a wanted status on a ship in many different systems and if they are wanted in that other system it will apply it so you know. This doesn't help you much in that its no justification in the eyes of the feds to shoot him down when he's in a different system to the one he commuted his crimes in..
You can still get the bounty if you go to the relevant faction to claim but you will get negative rep for the faction that the ship is registered too, when you kill it.... UNLESS he is wanted in the system you are currently in
For advice, the best way to get those prates is to go to the USS, unidentified signal sources.. These usually spawn mission critical stuff if your in the correct system.. (USUALLY)..
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The reputation system is absolute crap.
I failed some missions and maybe got scanned a few times with illegal goods. Now every federation ship attacks me. If I actually manage to get a mission for a federation faction they are now even harder to complete. If I drop out of hyperspace to kill some pirates there's now always additional ships attacking me which makes it even harder to not get destroyed and loose even more reputation.
I just started playing and am still deep in federation space.
Clear save is the best thing for you right now buddy specially if you juststarted playing m8..