Hi there Gino,
I've been through this recently, here's what I learned...
Like you, I installed a Pertronix unit in a 6V car. My problem was that while the starter was cranking, the voltage would drop below the
5V required to trigger the unit so no spark was generated. Once the key was let off the starter, the car would often (but not always) start right up - i.e. it would only start after, but not during, cranking. So if you have a voltage drop during cranking, you experience this problem.
If you connect a jumper wire from the battery cable at the regulator to the positive terminal on the coil (just a length of wire with an alligator clip on each end), you'll probably find it starts up immediately (but obviously you can't leave it like this or your coil would receive power all the time and burn up). But it can help with your diagnosis. Try and measure the voltage at the positive terminal on the coil while the engine is cranking over and see what its dropping down to.
The supplier of my pertronix unit told me that the module needs 5V to 'trigger' the spark, so on a 6V system you can't afford to lose ANY voltage at all, even with a 6V system in absolutely tiptop shape its a pretty close thing. Less than 5V and you just get nothing - which is why it doesn't fire up. With breaker points, even with a voltage drop, you still get some class of spark and its enough to get started with.
I found a replacement battery helped a lot (but my old battery was VERY tired), but has not cured the problem completely. If the car has been sitting for a couple of days or is cold, I still have to use the jumper wire trick. If the car is warm and has been out and about during the day, it starts up fine with just the ignition switch.
I also found that running an additional earth cable from the lower starter motor mounting bolt to the battery earth post helped a bit too. Make sure your gearbox to chassis earth strap is in good shape and that the connections are clean. In fact go over all your old wiring and ensure the connections and grounds are clean and bright - this seems to be mandatory for a functional 6V system anyway.
In my case, the ignition switch wasn't the problem but my reading (and Speedy Jim's suggestion above) indicated that the switch is often a cause of voltage drop or resistance in the starting circuit. They just get old.
I have found that the jumper wire from the regulator to the coil starts the car immediately every time and I am now thinking about trying to hardwire it in permanently with a 'momentary-on' switch so that I can deliver the extra squirt of volts required by the pertronix just during cranking to start the car and then release it without having to dive back into the engine bay whenever I want to start the car. Its just not a good look ;-)
Even with the difficulties in running the electronic ignition on a 6V system, I'm delighted with its performance and wouldn't want to go back to points. As you say, once the engine is running it feels strong and smooth and the timing is rock steady.
Good luck!