In previous problems that sounded like this one the problem turned out to be that the teams had been in leagues that were deleted. In setting up your Big 10, Big 12 leagues, did you start by creating generic feeder leagues, then edit them to be real-life conferences? Trooper College may've been in a league which no longer exists.
Could this be in any way related to the thread originator's problem?:
http://www.ootpdevelopments.com/boar...d.php?t=148284
I know this issue has nothing to do with phantom scheduled games, but if it connects to phantom teams…