Whever I've been suspicious of ignition problems I've always done the following:
1. Pull out all the plugs, put them back in the coilpacks & lay them on top of the cam covers (so that the coilpacks & plugs have a good earth connection).
2. Disconnect the starter motor power (so it can't be accidentally run)
3. Switch the ignition to ON
4. Turn the motor over slowly by hand (socket on main bolt)
After about 2 revolutions, the spark plugs will start to fire as you rotate the engine. The order is (as you'd expect) 1 5 3 6 2 4.
If you still get this strange multiple spark problem then something is wrong with either the ECU or Ignitor. If some of the sparks appear 'weak' compared to the others, then it is probably just time for new plugs (1Js have a healthy appetite for new plugs).