What year is this truck? I ask because I had an '03 that had this issue - brakes and one turn signal worked fine, one turn signal was inop on the trailer, though everything worked fine on the truck. Chased the problem for a long time, the dealer finally put a Ford computer in it that basically bypassed the existing turn signal circuit and combined it with the brake circuit. Fixed all the issues.
About a year later I was working on something and had to pull the fuse box under the hood...and found an additional relay/fuse combo, and as I looked into it I learned that some wires were chaffed through. So the previous owner had the issue pop up, and had the relay/fuse combo installed to fix the truck side but didn't worry about the trailer plug. I never bothered to mess with putting things back to factory because the Ford computer fixed all the issues, but I guess I'm pointing out that you could be fighting something similar under your fuse box.