Trailer turn signals work. but markers lights do not?

To the dealer or some other qualified repair shop. Light's are controlled by SJB - smart junction box , ford's body control module .
Principles of Operation
The smart junction box (SJB) monitors the headlamp switch position by sending voltage reference signals on multiple circuits to the headlamp switch. At any given time, one of the signal circuits is routed to ground. If the SJB does not detect any of the inputs to the headlamp switch is active (routed to ground) for 5 seconds, the SJB turns on the exterior lights and keeps them on for 10 minutes after the ignition switch is turned off (or 10 minutes from the time the SJB does not detect any headlamp switch input if the ignition switch was already off). If the SJB detects multiple circuits short to ground, the SJB implements a planned strategy depending on the multiple inputs received. If either of these situations occur, the SJB should NOT be ruled immediately as being at fault. This is normal behavior of the SJB design as it has detected a fault with the inputs from the headlamp switch.
When the SJB receives an input from the headlamp switch indicating a request for the parking lamps, the SJB energizes the parking lamp relay (internal to the SJB), which supplies voltage to the exterior lamps.

• One or more parking, rear or license plate lamps is inoperative

• Fuse
• Wiring, terminals or connectors
• Bulb holder
• Rear lamp assembly (vehicles without pickup bed)
• Cab marker lamp
• Trailer tow exterior mirror (if equipped)
• SJB

• Go To Pinpoint Test O .

Pinpoint Test O: One Or More Parking, Rear or License Plate Lamps Is Inoperative
Refer to Wiring Diagrams Cell 92 , Parking, Rear and License Lamps for schematic and connector information.
Normal Operation When the headlamp switch is placed in the PARKING LAMPS ON position, the smart junction box (SJB) provides a ground for the parking lamp relay coil (integrated into the SJB). When the parking lamp relay is energized, voltage is routed through circuit CLS30 (VT/WH) to the front, rear, license plate, dual rear wheel marker, trailer tow exterior mirrors (if equipped) and cab marker lamps (if equipped). Ground is provided to the rear and license plate lamps through circuit GD176 (BK/WH). Ground is provided to the LH and RH front parking and side marker lamps through circuits GD122 (BK) and GD124 (BK/VT), respectively. Ground is provided to the trailer tow mirrors through circuit GD179 (BK/VT). Ground is provided to the cab marker lamps through circuit GD115 (BK/GY).

This pinpoint test is intended to diagnose the following:
• Fuse
• Wiring, terminals or connectors
• Bulb holder
• Rear lamp assembly (vehicles without pickup bed)
• Cab marker lamp
• Trailer tow exterior mirror (if equipped)
• SJB
• PINPOINT TEST O: ONE OR MORE PARKING, REAR OR LICENSE PLATE LAMPS IS INOPERATIVE CAUTION: Use the correct probe adapter(s) when making measurements. Failure to use the correct probe adapter(s) may damage the connector.
  Test Step Result / Action to Take O1 DETERMINE IF ALL THE PARKING LAMPS ARE INOPERATIVE
  • Key in OFF position.
  • Place the headlamp switch in the PARKING LAMPS ON position.
  • Are all the parking lamps inoperative?
  Yes
  VERIFY the SJB fuse 22 (15A) is OK.
  
  If the vehicle is equipped with cab marker lamps, GO to O8 .
  
  If the vehicle is not equipped with cab marker lamps, VERIFY the SJB fuse 22 (15A) is OK. If OK, GO to O2 .
  
  No
  If the cab marker lamps are illuminated and all the remaining parking lamps are inoperative, GO to O2 .
  
  If all the cab marker lamps are inoperative, GO to O3 .
  
  If both trailer tow mirrors are inoperative, GO to O5 .
  
  For all others, GO to O6 .

The turn signal bulb circuit on the trailer MUST match the towing vehicles turn signals. Example: Tow vehicle turn signal light is the same bulb as the brake light, then the trailer must match. If the tow vehicle has a separate turn signal (amber bulb located away from the brake light) then an adapter is available that will send the correct power to the trailer so everything works correctly. The adapter can be found an auto parts stores, RV supply stores and some truck stops too.

Check the bulbs and grounds at the trailers marker lights.

Troubleshooting No Running Lights on Trailer but Turn Signals and Brake...
http://www.mastercraft.com/teamtalk/archive/index.php/t-17703.html
Thread Running lights on trailer don work but turn signals and brakes do

I would try hooking the trailer up to another vehicle and see if everything works right if everything works on the trailer I would start testing the trailer plug on your truck could be a wire has broken.

Exterior lights are power by tow vehicle, or you can hook to 12Volt battery or charge circuit. When your unit is plugged to hydro you should have one tab on tow plug that has +12vdc coming to it from converter circuit in trailer. Find that with a test light or meter, then when your sure you have proper wire in plug for running lights, use a jumper wire from one to the other to power lights temporarily while you find each problem with running lights .

I have the same problem.

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Trailer Wiring Diagrams 4 Way Systems

4 way flat molded connectors allow basic hookup for three lighting functions; right turn signal / stop light (green), left turn signal / stop light (yellow), taillight / license / side marker (brown) and a ground (white).

4 way tow vehicle side.
4 way trailer side.
5 Way Systems

Same as 4 way system listed above but adds a extra blue wire for brake signal or auxiliary power. Used on pop up camper trailers or utility / boat trailers.
5 way tow vehicle side.
5 way trailer side.
6 Way System, Rectangle Plug 3/4 inch by 1 inch 6 way rectangle connectors right turn signal (green), left turn signal (yellow), taillight (brown), ground (white). The red and blue wire can be used for brake control or auxiliary. Use on a small motorcycle trailer, snowmobile trailer or utility trailer. Can also be used as custom wiring on trailers with 3 light/wire systems. See "Tow Vehicle Taillight Wiring" below.
6 way tow vehicle side.
6 way trailer side.
6 Way Systems, Round Plug

Round 1 1/4" diameter metal connector allows 1 or 2 additional wiring and lighting functions such as back up lights, auxiliary 12v power or electric brakes. Note: The black (sometimes red) 12v and blue electric brakes wire may need to be reversed to suit the trailer. Check with a test light or VOM. Uses: horse trailer, travel trailers, landscaping trailer, car trailer, etc.

6 way tow vehicle side.
6 way trailer side.
7 Way Systems

Round 2" diameter connector allows additional pin for auxiliary 12 volt power or backup lights. Uses: heavy duty landscaping trailer, car trailer, boat trailers, horse trailer, travel trailer, construction trailer, etc. Check with a test light or VOM.

7 way RV flat blade tow vehicle side.
7 way RV flat blade trailer side.

check wiring on trailer

Did you check bulb in trailer.. Some have multiple elements for brakes and signals.. One can work while the other dosent.. .

so, the trailer has no brake lights, or turn signals, just tail lights? Everything (all lights) on truck work ok? What do you have for trailer wiring hook up 4, 5, 6, or 7 way? There is no fuse, the lights all work off the tow vehicle lights, so if the tow vehicle lights all work properly, it's probably a wiring problem, such as bad grounds, loose connections, etc. Get a volt meter and check voltage at truck plug to see if power is getting that far. If truck plug in is ok, wiring problem is the trailer. Make sure all grounds are tight and rust free, that's a common problem.