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Here are some helpful wiring diagrams.
Double check everything is connected the right way.
http://www.etrailer.com/faq-wiring.aspx
If the trailer was relying on the ground through the ball then what you did by running separate grounds to each light did not solve the grounding through the ball problem. You have to run the ground through the trailer to vehicle connector and make sure both the trailer and vehicle side have good grounds.Had similar issues with my last trailer. Finally discovered that it was depending on the ball on the hitch as a ground. Created my own ground by crimping an, "eye," on the ground wire, drilling a hole in the trailer in a hidden spot, sand it down to bare metal, and ran a ground to each light from there. Don't forget something like dilectric grease to keep corrosion from accumulating.
You have to run the ground through the trailer to vehicle connector and make sure both the trailer and vehicle side have good grounds.
Not necessary at all to run separate grounds to each light. The problem with doing that is that you have doubled the number of wire connections that you now need to worry about. If you start with good bare grounds at every light, you will never have a ground problem at a light assuming you have a trailer whose frame isn't a bunch om metal bolted together.