Based on your description of the problem I would trouble shoot the electrical issues before I replaced the controller. Follow your symptoms of the problem with the turn signal etc. As your gut told you that is not right.
If you have a volt meter or test light. Unplug the trailer from the Tow Vehicle and test the receptacle at the Tow Vehicle. Check the brake positive feed for voltage flux when the turn signal is turned on. I expect none but that helps you determine if the problem is with the Tow Vehicle or the trailer. I am guessing (that is all just a guess) you will find the problem under the pin in the junction box or worse with the wiring for the trailer.
Good luck and please keep us advised.
Cheers,
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