I have played 8 NCAA super championships over the years using Dave's Pre and Post 1970 greatest teams. 1945 Alabama has been dominant winning 6 Pre 1970 titles and 5 Super Championships. 56 Oklahoma has posted 3 perfect regular seasons but hasn't had any postseason success. 61 Texas and 59 Syracuse have captured the other two Pre 1970 crowns.
The Post 1970 competition has been more balanced. 71 Nebraska and 89 Miami have two titles each but neither has won a Super title, each losing twice to 45 Alabama. 76 Pitt, 98 Ohio State and 73 Alabama have won the other three Super Championships. 73 Alabama handed 45 Alabama their only Super Championship game loss. 94 Penn State also won a Post 1970 title but lost to 45 Alabama in the Super Championship.
I was wondering if 45 Alabama has been as dominant in some of your replays.