Sequential tail light help...again

I know, I know, there are a million threads about them, but none seemed to answer my question. Here's the deal

I'm a tech at a ford dealer. A guy traded in his 06 mustang GT, which had sequential tail lights. He bought another car, and had no use for them, so I asked the salesman who delt with the customer if he wanted them back, customer said no, so I yanked em out. A year goes by (as of yesterday) and I finally installed them. They where a plug and play style for the 06, so I cut the modules out of the harness, and followed the instructions on American Muscle's website for installing them on 96-04 vehicles. The modules looked the same (black pill looking shape with 5 wires coming out) Wire colors where even the same for both styles for 05-09, and 96-04, so I figured no issues. I did the passenger side first, twisted wires together to make sure it worked, and it did, so I soldered everything together. Did the driver's side one, and for some reason, it doesn't work all that great.

The problem is, The outside 2 lights flash at the same time. The inside one will flash first, then the outside 2, at the same time. I checked all my wiring, everything is okay. I started the car up and checked again, and all of a sudden, it works fine. Now, I don't really care that it doesn't work when the car isn't running, because, when am I going to be turning left, when my car isn't running? haha, But for anyone that knows me, knows that I'm particular about my car, and I just would rather it work the way its supposed to. Anyone have any suggestions?
 
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I can think of 2 possibilities:

-1- One of the modules is sensitive to voltage. The system voltage will be higher when the engine is running (14V-16V versus 12V-13V).
-2- There is excess resisitance in the the turn signal wiring and/or switch on one side.


I would try swapping the left and right-side modules to see if the problem moves with the module, or stays on the Driver's side. If it moves with the module, there's probably not much you can do about it other than replacing that module with a new one.