Flunkgate and the probation were 2 different things.
Flunkgate was due to, literally, Gailey treating the players like adults. He trusted they were going to class, study halls, and that the academic support staff were doing their jobs. They weren't.
The probation happened because Frank Roper, the academic supervisor of eligibility, was about to retire, was old and ornery and thought he knew everything (I know...a Georgia Tech man thinking he knows everything...never happens, right?). He quit going to the annual NCAA meetings and missed the requirement that changed where they said that athletes now had to be eligible using the stricter of your school's requirements or the NCAA requirements. Tech's are more stringent than the NCAA's and while our athletes were eligible by NCAA standards, they weren't by Tech's standards.
Someone finally caught it and Tech self-reported to the NCAA but was penalized.
ONE IMPORTANT NOTE HERE, GENTLEMEN: In both cases, the people who were appointed as academic support staff BY THE HILL were either the main culprit or at least a contributing factor in each of those 2 problems.