In LIVE play, when a potential base stealer is on, you have the option to HOLD the runner close to to the bag. In fact, when playing against Sparky during a LIVE game, he almost always uses HOLD when even an outside threat is on base. The downside of HOLD is that it draws the pitcher's focus away from the hitter, slightly, and gives the batter a better chance in the PA.
Could this be yet another reason why SB and speed teams tend to excel in leagues? LIVE play is the exact same engine, after all.