Steve Bowden posted a detailed description of the bug on the PAPA Blog. I've copied it below. It's the best explanation I've seen so far.
I believe the key to the “glitch/feature” is at 5:24 when he locks a ball with 0 seconds left.
Starting at Multiball stage one, the game thinks there are three balls in play. (correct)
Two balls are locked. (so far, so good)
Here is where the conflict might have happened.
1. There are 0 seconds left, so it’s time for the game to release the balls for a retry. Stage one continues albeit VERY briefly. A ball was locked in the skull immediately (after the hypothetical release that didn’t happen), so lets go for the Single Jackpot. The other two balls are out of play.
2. Ball 3 is locked! Let’s go for the Triple Jackpot!
Where the cross-up happens is hard to know. Regardless, the game is playing the “Big Shot Jackpot tension music” so we are good there.
So, I guess there is a “fight” in the programming between:
1. The timer ran out and one ball was locked immediately after that. Give him the 7.5 million Single Jackpot, and let’s go back to single ball play.
2. Three balls were locked! Give him the 22.5 Million Triple Jackpot, and let’s go to stage 2 to go for some Super Jackpots!
4. Result: Award the 22.5 Million but go back to single ball play. However, move forward to the stage 2 Multiball music.
Now, the game is in stage 2 for the Super Jackpot attempts. The game’s soundtrack agrees with this, since it is playing the stage 2 music. But, the game also now thinks he is back to single ball play where you need to re-lock the balls (because there were 0 seconds left on the timer from before).
Then, a ball is locked in the skull.
1. Let’s go for the 2 targets to start the next multiball.
2. Let’s go for the Super Jackpot! (But, it’s still playing the multiball stage 2 music, and not the “Big Shot Super Jackpot tension music”)
The target for the Super Jackpot happened to be one of the two needed for the next round of 2 mutiball targets. RESULT: Give him one of the two targets.
I may be off-base since this is conjecture and theory. However, this is based on what I have seen when playing the game. I think I remember having some of the same strange behavior when I have locked a ball on T2 with 0 seconds left on the clock.
By the way, a little bonus glitch: At 20:37, after Josh does not relock the ball to go for a Single Jackpot, the game is still playing the music for Multiball stage 1 when Josh is in single ball play. Yes, I like pinball music THAT much. ^_^