Kawboy, pretty damn good explanation, but a lot of possibilities left out! And here's where it gets complicated to explain in print on a forum. But, just one possibility would be if the insulation of one spark lead were to break down and leak to ground, that would weaken the spark energy to that plug, but COULD actually decrease the overall resistance in the WHOLE circuit, causing a stronger spark in the other lead from that same coil. Gotta keep in mind that if all parts of the circuit are in good shape, the current in all sections of the circuit will be the same, meaning that the spark intensity will be the same. But, shunt some of that energy to ground at any point and you imbalance the system, causing one spark to decrease and the other to possibly increase from a decreased resistance in the system overall.
There would be about three more volumes to cover all of the other possible issues that could happen in these silly double-ended coil systems!
BTW, somebody on here was talking about their bike popping on deceleration recently. This "wasted spark" system is partly responsible for that, too! When you close the throttles, there is an initial small surge of fuel that has no air to burn with it, so when the exhaust opens up it goes out unburnt. Well, that "wasted spark" sometimes catches the tail end of that batch of fuel and ignites it along with some of the incoming air/fuel during the valve overlap period. There is a lot of air in the exhaust to allow for combustion, so you will get a pop once in a while, or when all conditions are favorable, a LOT of the time! Just watch the exhausts of some of the higher-powered GT race cars as they enter a turn. Their valve overlap is so great that they burn a LOT of wasted fuel this way, and it causes more than just a simple pop! Huge flames shoot out!
Oh, we could go on and on, but,......!