pa23driver,
Well, it would help if we knew what year / model bike you have and why you decided to use a dual output coil with points and what the part number is for the coil and whether or not you installed a new set of points and condenser.
Without all of the above, my first thought is that a dual output coil produces a positive voltage on one plug and a negative on the other. The timing light only works properly on the negative wire, but there is no easy way to determine which is the negative wire, so all you can do is swap the timing light to the other wire. One of the problems with using the timing light on the positive plug wire is that the timing light will fire on the trailing edge of the spark, which occurs later than the leading edge, so it could show up at TDC.