I don't know about secondary lighting, but if you're running two lights from one 6v generator, aren't you going to overload it? It's only a guess, but is it possible that the Schmidt Dynohub is clever enough to include an overload cut-off device in its circuitry?
Let's say your lights are 0.4 amps, and you're generating 6 volts at 3w (again, guessing, but this is fairly normal), then you'll end up drawing 4.8 watts from a generator rated at 3 watts. Unless there's something about secondary lighting that I don't know.