By switching a shorting connection 100's of times per revolution, the caps will charge beyond that certian level and faster.
I've looked this one over fairly thoroughly, and have come to one conclusion.
Effectively, what you have is called a "magneto", just like the one in your handy-dandy lawnmower that provides the juice for the spark plug to fire.
The voltages are a little different, but the principle you're seeing is almost certainly (from what I can gather) exactly the same.
In a magneto, a magnet comes by, polarizes an armature with two coils on it in one direction, while holding the "primary" coil shorted. As the magnet passes, the coils are arranged in such a way that the magnetic polarity in the coils suddenly flip *hard* the other way (Disclaimer: Depending on the exact design, it may or may not actually flip just prior to the next part). At that moment, a switch (called the "points") holding the primary shorted opens up, and the magnetic field collapses violently, cutting across the secondary coil and thus firing the spark plug.
So, what you've "discovered" is an age old trick with magnetic fields used for creating very high voltages with a very simple mechanism.
But as a generator for charging batteries, the technology is just about useless, unless you have something like a 15kV 2mAh battery laying around to charge with it.
Probably not the case. But I do however admire your perseverance...