We can see all of the current season's progression, which shows the difference in development effectively enough. Patience and Temper might have something to do with it, and their influence could have been part of the unspecified development changes made in the last update. Because their OVRs went up almost the same amount, it's possible that Flores' growth is exaggerated a bit and Belliard's downplayed a bit by rounding (Flores' 78-85 development in Control might actually be 78.9-85.0, while Belliard's 75-80 could be 75.0-80.9; I don't think anyone has ever nailed down how they round off numbers, but what appears to be a 7:5 development difference might actually be 6.1:5.9). I'd also guess that as a 1-3 pick Flores' projections were indicative of big development, particularly if you had high scouting when he was drafted.
In the last Developer Chat they said appearances matter, not innings. There's a lot of doubt whether that's accurate, but if it is their difference in Games (30-28; 6.7%) is much smaller than in Innings (180-140; 22%). If the answer was accurate, Belliard's significant Innings advantage becomes an insignificant games difference.
And as dedelman said, stuff happens. A season is a small sample size.