So, the young manager made the decision to fine future superstar Derrek Lee after the 18-year-old got hung up in his native Sacramento, Calif., missing the first practice for Rancho Cucamonga, then the Class-A Advanced affiliate of the San Diego Padres.
More than 15 years later, Flannery still laughs when recalling the incident, and he has no qualms with how his punishment was received.
"At that point you are trying to feed everybody," Flannery said. "I knew he was the [Padres'] No. 1 pick. I knew he could at least afford to buy the boys chicken and pizza."
But by the time the season ended in Rancho Cucamonga, Lee hadn't just provided chicken wings and some good-natured ribbing; he had emerged as a man in every sense of the word.
The most obvious difference was in his physique, a transition Flannery remembers as stark and sudden, not unlike any teenager's transition to becoming an adult. Except with Lee, the stronger he got physically, the more important his mental toughness -- a subtle but steady part of his game -- proved to be.
"That's something that separates the superstars from the real good players," Flannery said. "It's the mental part of it, and that's his strength."
Both Lee's father and uncle played baseball in Japan for nearly a decade, and Derrek's natural abilities were highlighted by his advanced knowledge of the game. Considered a blue-chip prospect, Lee was one of a handful of high school hitters -- joining Major League veterans Alex Rodriguez, Torii Hunter, and Trot Nixon -- to be selected in the first round of the '93 Draft.
In his first stint as a professional, Lee played in 15 games for the Padres' rookie team and was named the Arizona League's top prospect before leap-frogging two levels and finishing the season with Rancho Cucamonga.
Under Flannery's watch in 1994, Lee batted .267 in a team-high 126 games, and he was second on the club with 118 hits. He overcame a sluggish start to help the Quakes stun the California League and win the championship after earning the Wild Card berth.
"The first half he had a big hole in his swing," Flannery said. "There was this big hole, but he worked at it and it just kept getting smaller and smaller until it disappeared."
Lee's swing wasn't the only change in the youngster's development. When a mid-season promotion left the Quakes down a first baseman, Flannery moved Lee, who was drafted as a third baseman, to the other infield corner.
The rest is history for the three-time Gold Glove winner, as Lee has been among the National League's top first basemen for the better part of the decade.
After earning back-to-back Minor League Player of the Year honors (in 1995 and '96), Lee struggled in the Majors following 1998's trade to the Florida Marlins. The 23-year-old opened the following season with Triple-A Calgary and persevered through a year of ups and downs before finding his stroke for good in 2000. Lee took home his first Gold Glove Award in 2003, providing stingy defense for the World Champion Marlins.
That season was just the start for the two-time All-Star, as Lee has also added a National League Batting title and Silver Slugger award to his ever-growing list of accolades.
"The greatest thing for me, especially now 15 years later, is he honors the game and he respects the game," Flannery said. "And what I've always been taught is, if you respect and honor the game you are going to be blessed by the game."
"I tell people all the time about him. [I say,] 'He's been an unbelievable player, and he's not even close to being done."