Did you start out with a fully-charged battery? 6 volt systems don't recover from starting loads nearly as quickly as 12V systems do, even generator-equipped ones. That system should have a 25 amp capacity generator, which will support the headlight load and ignition with a very little bit of amperage left over to charge the battery. A fully-charged battery is essential to proper operation of a 6 volt electrical system, particularly if it's not a daily driver!
Jerry