I had the same experience on Elliott Bay with a freighter that was in the middle of finishing a turn while accelerating. I was delivering a 44' heavy wooden ketch and looked over my shoulder as the ship went by, just in time to see a very steep breaking wake heading our way. Turning into the wake we plowed through taking water over the entire deck, through any open portlight in the cabin and filling the cockpit with several inches of water. I've had the same boat in gale force winds and never come close to taking water aboard like that.
It just shows we've always got to keep our eyes open and realize it often doesn't take much of a difference in conditions to make a huge difference in the outcome.
I'm guessing it was a combination of current against wake plus the acceleration and turning of the ship all happening at the same time.
Sea Kayaker Magazine