NEW YORK — The Matsuzaka Mystery of the 4th Inning reared its ugly head again last night, for the second time in his last three starts.

Daisuke Matsuzaka pretty much sailed through the first three innings, scattering two singles and a walk and working around an error in blanking the Yankees.

But then came the fourth inning.

Suddenly, Matsuzaka’s command seemed to leave him, just as it had in the fourth inning in his start in Toronto on April 17. In that game, he threw 38 pitches in the inning and wound up giving up two runs, walking three, forcing home what proved to be the game-losing run with a base on balls.

Last night was worse. The bottom line was four runs, three hits, three consecutive walks and a whopping total of 41 pitches.

It started with a walk to Alex Rodriguez. The key pitch was a 2-and-2 fastball. Matsuzaka, after lulling the Yanks to sleep with 91- and 92-mph heaters, sizzled this one to the plate at 96. But A-Rod is on top of his game now, and he fouled it back, eventually working a walk.

That’s when Matsuzaka lost his command. He walked Jason Giambi on four pitches that weren’t even tempting. That prompted a visit from pitching coach John Farrell, but it didn’t help Dice-K’s control.

Hideki Matsui worked an eight-pitch walk, filling the bases. A strikeout of Robinson Cano, with J.C. Romero starting to get loose, and a Doug Mientkiewicz popup almost had him out of trouble, but Johnny Damon’s half-swing single and Derek Jeter’s single accounted for two more runs and a 4-2 New York lead.

Finally, on his 41st pitch of the inning, Bobby Abreu flied to shallow left.

As the fourth went on, no one was up in the bullpen, with manager Terry Francona trying to remain patient, remembering that in Toronto, after his fourth-inning doldrums, Matsuzaka was unhittable in his final two innings.

Matsuzaka, meanwhile, was clearly uncomfortable. At times he paced around the mound, rubbed up the baseball, took off his cap, wiped sweat from the back of his neck, obviously trying to figure out on the fly why things were unraveling.

It was thought in Toronto that pitching out of the stretch ruined his rhythm. He didn’t do anything in the fourth to dispel that notion. But, mystifyingly, over the first three innings, the Yanks were 0-for-7 with Matsuzaka pitching out of the stretch. Only one batter reached, on an error.

What happened in the fourth also was at odds with the way Matsuzaka began the game, going to 0-and-2 counts on 7 of the first 10 batters he faced.

Matsuzaka lasted two more innings, a victim of the pitch count he had driven up in the fourth. He wasn’t dominant, but he retired the side in each of the fifth and sixth innings, finishing his night with a season-high 117 pitches. He left with a 6-4 lead.

Whatever “disease” Matsuzaka caught in the bottom of fourth apparently was contagious. Yankee starter Andy Pettitte threw 37 pitches in the top of the fifth (four walks) before being lifted, having coughed up three runs and leaving the bases loaded for Scott Proctor.

Proctor needed only one pitch (Coco Crisp flyout) to get out of the jam, but the Sox were on top, 5-4.

Good idea, Julio

You have to touch ’em all to get credit for a home run.

Julio Lugo doesn’t hit many home runs — he had 68 in 920 games heading into the season — but he is well aware of the concept.

So when he rounded the first-base bag in the sixth, not knowing if his drive to left would go out, he cut the base close. He was a few steps past the bag when he saw the home run signal from the umpire, the ball having just cleared the left-field fence.

Just to make sure he had indeed touched first, he went back and tagged the bag, and then took off on his home run trot. It was his first homer of the year.

Shift variation

The Yankees’ shift for David Ortiz with nobody on base early in the game was a little different than the one most teams use.

Jeter, the shortstop, was not swung over on the second-base side of the bag. In fact he was several steps over on the shortstop side of the base.

The reason was that the Yanks had a left-hander (Pettitte) on the mound. They didn’t expect the Red Sox’ designated hitter to pull as often as he does against right-handers. In the third, Ortiz grounded out to Cano, the second baseman, who was playing a few steps on the outfield grass, but basically in his normal spot between the first and second base bags.

The infielders were deployed the same way when he faced left-hander Sean Henn in the sixth. Ortiz walked.

Earning his keep

There were some eyebrows raised in the offseason when the Yankees signed free agent first baseman Doug Mientkiewicz.

Clearly, his offensive skills have been in decline.

But in the first inning last night, Mientkiewicz offered two reasons why he can be an important member of this team, even if he struggles to bat .200.

On the first batter of the game, Mientkiewicz was able to dig out a low throw on the backhand from shortstop Jeter. Then, with two outs and two on, he stayed with J.D. Drew’s top-spin, short-hopper, trapping it with his body, picking up the ball and beating the hustling Drew to the bag for the final out.

In the third, he scooped a short hop from Jeter, who was throwing on the run as he raced in, saving him an error.

Mientkiewicz still is a quality defensive first baseman. A year ago, third baseman Alex Rodriguez and Jeter made errors by the bushel, partially because of having Giambi and others at first.

Now, they have peace of mind and can just let the ball go, without thinking about having to make the perfect throw, and that will be a help to the Yankee infield in the long run.

skrasner@projo.com