Start with basic troubleshooting. Are the truck brake lights also on when the gain is turned up? Unplug the trailer, are the lights still on? If not, check for a short in the trailer wiring, some feedback loop or something triggering the brake lights. If the trucks lights come on when turning up the gain, then there is either a controller issue, or a harness issue. What does the dash say when you look at the trailer settings, is it properly setup for the type of brakes, Electric, electric over hydraulic, Surge? It's either a wiring issue, bad controller, or a programming issue.

 

Truck brake lights are also on. Doesn't matter if the trailer is connected or not when the gain is above 0.5. Anything equal or greater than 0.5 the trailer and truck brake lights come on and when the trailer is disconnected, the truck brake lights still come on.
It also doesn't matter if the effort is low, medium, or high. I have electric trailer brakes and have that selected.
As prev mentioned, I took the cover off the brake controller and it does appear to be an OEM Ford break controller.
Still have to use the aftermarket Reese controller.

When connecting the USB device to the truck using Forscan, it does mention that the USB dongle isn't fully compatible and that some commands/programming might not work. Maybe it's the USB dongle I bought? I got from Amazon.

 

I called the Ford dealer to get the part number they say works with the truck. They said HC3Z-2C006-AA is the correct part number.
The part number on the controller I have is HC3C-2C006-AD3JA6. The eBay ad the guy posted said it is part number HC3Z-2C006-AA. I don't doubt it is the correct part.
I think my best option is to take it to the dealer and have them program it for me.

 

I did some more research on ChatGPT. Comparing the different part numbers, it said "Since you're installing in a 2019 F-250, verify whether your truck has the Tow Package (look for the fuse or wiring under dash). If it does, go ahead and use the 2C006‑AA. If not, either install the necessary fuse/relay or use the 19H332‑AA which likely already includes them."
and
"You can use either brake controller part number in your 2019 F‑250, provided:

• Your truck has the Tow Package (fuse and relay already installed).
  
• Or, if you don’t have the Tow Package, you must add the missing fuse/relay when installing the 2C006‑AA version."
  

and
"What’s Different
According to Ford Truck Enthusiasts and F‑150 Forum discussions, the 2C006‑AA version typically does not include the fuse and relay required if your truck lacks the Tow Package wiring. The 19H332‑AA may include those components"

It says I need to check to see if I have fuse F29 and relay R15 (verify on model year/owner's manual). If missing, add them. F29 is a 30A fuse and R15 is the relay that allows the trailer brake controller to send power to the trailer. I do get power to the trailer, as the brakes are fully applied (with the brake lights on) at any gain setting of 1.0 or higher. The part number for the relay is G8HL-1C4T-R1.

I checked my owner's manual and the slots are different for mine.
My appears my truck does have both the relay and the fuse in the box under the hood.
The trailer brake controller related items in fuse section of the owner's manual are:
#27 - 30A Fuse - Trailer tow battery charge relay (if equipped) - My truck has this slot populated
#37 - Trailer tow battery charge relay (only on non-trailer brake controller vehicles) - My truck has this slot populated
#42 - 40A - Trailer tow lighting module (if equipped) - My truck does NOT have this slot populated
#54 - 30A - Trailer brake control module - My truck has this slot populated
#65 - 30A - Trailer tow lighting module (if equipped) - My truck has this slot populated
#72 - 30A - Trailer tow left hand/right hand stop/turn (if equipped. not present with trailer brake controller) - My truck has this slot populated
#84 - 10A - Trailer tow backup lamps (if equipped) - My truck has this slot populated
#99 - 30A - Trailer tow parking lamps - My truck has this slot populated

Does it look like my truck should have all the tow package stuff? One thing that has me questioning is #72. It says it is NOT present if it has a trailer brake controller. I took that fuse out but it made no difference.

One other thing I just noticed, when I set the gain to 1.0 or higher, on each side brake light of the truck, instead of both light bulbs in each light coming on - an upper lamp on one side and a lower lamp on the other light come on. The high center stop lights also comes on.

 

That Forscan dongle may not working correctly, when programming.

I would recommend this one
No need to manually switch between CAN buses, works perfectly.and is recommended by the Forscan people.

 

I’m a little confused so the part number on the controller doesn’t match what Ford says is correct, but the seller says it’s the same? I dunno. Most of the fleet package base XLs don’t have tow packages. It should be listed somewhere on your window sticker (thought I saw you had it).

You’ve accumulated likely more knowledge of your situation via the web than I’ll know.

I’m not a wiring expert by any means and these trucks are so sensitive I won’t hardly mess with them. If your opposite brake lights are working I’m guessing you have a short or grounding issue somewhere (could be anywhere) that is triggered by the brake controller activating. I had a lot of goofy issues happen to my truck and it turned out to be a wiring issue. Caused a lot of problems including the opposite/half brake light malfunction (turn signal as well) that you’re seeing. Mine is a Lariat ultimate with a lot more options so maybe you won’t see as many issues. Make sure all the trailer plugs are good. I think a factory integrated controller is probably a lot more sensitive to an issue than your Reese.

 

There has been many problems reported with the 7 pin wiring connector plugs behind the rear bumper. They were creating havoc with the electrical system.

Maybe check that.

Moisture and dust needed to be cleaned and seal the plugs with dialectic grease.