Soooo, really old thread but I just had the same thing happen to me with the exception that I did hear the victory call-out and saw the invasion won animation, point total, and wizard mode board clearing.
V.5.0 rom, no known switch errors.
I was having a terrible invasion and was still on stage 1 with ~15 seconds remaining, one ball was locked in Otto and the other on the upper playfield. After hitting a stand up target, suddenly the flippers died and it said I won with just over 6M points total.
It was my first go at AI during that game and I never made it past stage 1 so the above theories don't hold. This is the only place I've seen this bug mentioned so I thought I'd mention that it happened to me too.