Most of the times when he's throwing a fastball, Matsuzaka pulls the baseball out near the tip of his glove in his windup. When he's throwing breaking pitches, he keeps the ball buried deeper in his glove. In the examples provided, it seems blindingly obvious, though some posters rightly wonder what the batter is actually seeing from his perspective.
This could be why Matsuzaka is far more effective when pitching with men on base, i.e., not from a full windup.
Batters vs Dice in 2009
PA AVG OBP SLG OPS
With Men On 146 .254 .345 .389 .734
With No One On 137 .398 .460 .683 1.143