I had exactly the same problem, in my case it was the brushes, if i cleaned the commutator then the problem would go away for a while, but it would return because the brushes were soft and quickly making the commutator dirty again.
So new brushes cured the problem, and so far so good.
I used a voltmeter to confirm the issue existed when the commutator was dirty, with F and D joined the voltage was around 0.4 v from memory even when blipping the throttle, and this was obviously not enough to get generating going, after a clean i was getting nearer 0.7volts at tickover and a blip on the throttle would make the volts jump to over 6v and stay there.
Edit: i have a dvr2, and 6v "motoblatt" battery