I'm nearly sure that was when the receiver (Atwell?) had clearly come down with his foot inbounds in the endzone and the ref called him out. After the game the ref claimed the color of the shoes was too close to the color of the sideline or something like that. Joe Pa went the to locker room as you mentioned and then blasted the officials in his post game news conference and got fined afterward. That was the second time the Gophers had gotten hosed, but this was more blatant and literally cost them the game.
I remember the Friday before the 1999 game I was talking to a coworker who worked in Atlanta and knew next to nothing about B1G football, just knew PSU was really good and MN was "not" (though they turned out to be better than people thought). He said something like "how many touchdowns do you expect to lose by?" and I said "Mark my words - the Gophers always play tough in Happy Valley. I'm telling you, it will be a close game. The Gophers got screwed the last two times out there. They will be in the game until the end."
My phone was ringing when I came in Monday morning. I literally answered it right before it would have gone to voicemail. The guy from ATL couldn't believe it. He said he figured I was full of crap (not a bad assumption), but as the game went on and the Gophers were right there, he started to believe. He actually turned the channel from his alma mater (Texas, if I remember right) to watch the end of the Gopher game so he saw the final drive. I almost think he was more excited about it than I was, and I was pretty darn excited about it.