I had a similar problem with our brake controller last fall. Check all the wires you can see for cracks and wear. If there is truly a short, it could be anywhere in the system... where the wires go into the axle tubes, inside the brake drums, at the connector, break-away switch, in the truck's wiring, etc.
For my situation... it was the controller. If you have another or a friend has one installed, try it out.
In my search, I tried isolating each axle/drum (by cutting the wires at the axle) and testing it out with my controller. Unfortunately, my short was intermittent and this test didn't get me anywhere. I didn't found a short at the axle tubes as others suggested. I pulled each drum to inspect the wires & magnet for wear... nada.
Finally, in frustration I bought another controller... problem solved.
Happy Camping!
John.