I had a very wierd problem also. I checked everything that people said it could be and still my bike wood not charge. It ended up being the wire from the regulator to the back of the diode board. It was heat damaged and barely hanging on inside the plug on the regulator side. It would give good meter readings but not pass any current. It was a very strange issue. Maybe try to check that.
1977 BMW R75/7
2004 Kawasaki Ninja 250R (Wifes)
1977 RD400 (for sale)
2006 Buell Ulysses