A lot of coils are designed so that the secondary winding is terminated at the battery connection. If the primary wires are connected backward, you get some 40 - 80 K-volts across the winding instead of the few hundred it was designed for. So, if the problem persists, try switching the low voltage wires.
Which brings us to another possibility. If the plug gaps are too wide or you have resistor type plugs and/or wiring and the wiring is old and tired, it can cause the voltage across the secondary winding to go so high as to break down the insulation.
