I don't think that the problem only happens when the pertronix is on there, its more that breaker points are more forgiving of low voltage than the electronic unit. With the points, even with low voltage you still get some class of spark and apparently enough to fire the engine whereas with the pertronix its all or nothing and low voltage equals no spark at all.But why it is only when you use the Pertronix baffels me.
I think putting the pertronix on has brought to light a problem that has probably always been there so this is a good opportunity to put it right.
Going to try and have the battery load tested today, if I can find a place that can test a 6v battery...