I drove around their parking lot (the size of a football field) with an automobile battery hooked directly to the feed to the brakes and then back it back into their shop, could not tell the brakes were on.
This does not make sense. Why not just hook up the trailer to your tow vehicle and use the boost value or manual override to test the brakes. Why the automotive battery apart from the tow vehicles battery system? Drive it ten or fifteen miles using the brakes a lot and see if they start working better.
Also, I second the previous poster's comments on the cost factor. You must be getting a gold plated service for that kind of cost.
Check to make sure the voltage is correct through your controller when you apply the brakes and check all wiring from the hitch to the brakes. What is your controller saying is the voltage to the brakes when you apply the brakes hard? Wiring sometimes gets damaged. Some have reported increased braking after upgrading the wiring to all four brakes with the next larger wire size.
Try pulling the brake away switch and see if the brakes grab. If the shop did the brakes correctly, the only thing left is the wiring.