I'm in the middle (60 games) of my third 2009 season. Season one: no balks by any pitcher on any team. Season two: ditto. Season three: ditto. That's nearly 40,000 IP -- more than 150,000 dice rolls.
I don't care about balks, but I do care about the game engine. This is clearly a flaw in the game engine -- and when there's one, there's probably more. Bernie's team really needs to look into this, solve it, and figure out if it has implications for other aspects of the game engine's reliability.