What type of signals are you adding? If it's a standard bulb, as long as you have a good ground and you're positive you have the right wire for the right turn signal it should run - regardless of which order you hook them up. If you're swapping in LED signals the polarity has to be correct. You could potentially have the correct wires hooked up (intent being to connect black to black and brown to red) but if they put the led in backwards at the factory it won't work. I had the problem with aftermarket gauges I put in one of my cars.
Try running a voltmeter on the wires to ensure that the diagram you have is correct. When you turn on the signal, you should see a jump. If you know you have the right wire there, check your ground.
If it's a standard socket type plug, can you swap it over to a three wire to keep the running lights? I imagine it'd be nice to have them.