It is very easy to confuse running with brake lights. I am wondering how you know the running lights are working if you don't turn the headlights on?
I am guessing you put the parking lights on???
You might have several things going on which makes it very hard to figure out. Here is what I do EVERY year because EVERY year I have to work on trailer lighting...just the way it is!
First grab or make up FOUR jumper wires....I have a nice set of alligator clipped wires to assist on this but any wires will work.
Take one of your sled batteries over to the wire harness and test the plug to the trailer. Hook the negative side of the battery to the trailer...making very certain you have a good ground going by shining up a spot on the tongue and grounding there...not on the plug wire, but straight to the trailer...this removes possibility of bad grounding wire.
Now process of elimination by touching each post of the harness to the positive side of the battery....use a mirror or a person at the rear of the trailer to report what they see.
Reminder...you have running lights post, brake light post and right and left posts. If this all works then you have an issue with either the connection to the car or the car wiring.
Oh...one more thing....be sure the bulbs are good...that can make for an extra hour of diagnosis if you don't have good bulbs. If your trailer is a tip type, there is a ground jumper from the tongue portion of the trailer to the rear portion of the trailer and THAT wire can get cut or corroded and may need to be reconnected to a good clean ground on both sections of the trailer.