Red Sox batter Mike Lowell is irate after a called third strike by umpire Marty Foster in the ninth inning of last night’s game. Holding Lowell back is manager Terry Francona.

The Providence Journal / Gretchen Ertl

For the last two months, the Red Sox had been waiting for the day when they could reunite their potent combination of David Ortiz and Manny Ramirez.

But last night, with Ortiz back in the lineup after an eight-week absence, Ramirez wasn’t.

Manager Terry Francona wrote Ramirez’s name into the lineup, which was posted when the clubhouse opened, assuming that the slugger’s knee was improved after Ramirez told Francona he was unavailable Wednesday in Seattle.

But while Francona spoke with reporters in a second-floor interview room, Ramirez informed bench coach Brad Mills that he was again unavailable, necessitating a revised lineup.

Minutes later, Francona appeared on the field as the regulars — minus Ramirez — took batting practice and summoned principal owner John Henry and chairman Tom Werner. The trio left the field and met behind closed doors in Francona’s office for an extended period.

Some skepticism exists within the organization about the severity of Ramirez’s injury. Ramirez did not seek treatment for the knee Thursday, an off-day, a signal to Francona that Ramirez would be available for last night’s series opener.

In an effort to determine what is ailing Ramirez, the Sox sent him late yesterday for an MRI at an area hospital, the results of which were pending last night.

Henry’s involvement in this could be telling.

For most of his ownership, Henry has been one of Ramirez’s biggest backers and has defended him in the face of Ramirez’s many controversies.

But when Ramirez complained to The Boston Herald during the All-Star break that the Red Sox and ownership had been less than forthright with him and he hoped they would be honest in communicating their future plans for him, Henry lost his patience.

He fired off am angry e-mail rebuttal to The Herald, telling the paper he found Ramirez’s remarks “offensive,” contending that the organization had always been honest with Ramirez.

This is not the first time Ramirez has sat out with knee soreness. He played little over the final five weeks of 2006 due to patella tendinitis in the left knee. At the time, MRIs showed some swelling, but no structural damage to the knee. Ramirez rehabbed the knee that off-season and reported to spring training in 2007 without any limitations.

The debate over how hurt Ramirez is comes in the aftermath of two off-field incidents involving Ramirez and others.

On June 5, NESN cameras caught Ramirez slapping teammate Kevin Youkilis, reportedly over Youkilis’ frequent outbursts in the dugout.

Then, late last month in Houston, Ramirez shoved traveling secretary Jack McCormick to the ground. Ramirez had made a late request for 16 tickets and when McCormick advised him that it might be difficult to fill, Ramirez exploded and pushed him before others could intercede.

Those incidents, along with Ramirez’s being unavailable for the last two games, may have altered the organization’s thinking on picking up Ramirez’s 2009 option, worth $20 million.

At the start of the season, it seemed a virtual certainty that the Sox would pick up the option for next season, given the lack of power-hitting alternatives on the market, and the fact that the Sox need commit to him for only the short-term.

Ramirez, meanwhile, has repeatedly said he hopes the Sox would offer him a contract extension past the second option year of 2010. Failing that, Ramirez has said, he would like to play elsewhere for at least four more seasons.

Ironically, if the Sox sour on Ramirez further and decide not to exercise the 2009 option — a decision they must make by the first week of November — such a tactic would free Ramirez to auction himself off to the highest bidder for a longer deal, one far more lucrative than the $40 million represented by the two options the Sox hold.

If Ramirez were to be granted free agency, the Sox would then be put in the position of searching for a hitter to pair with Ortiz in the heart of the batting order.

The fact that the team survived the loss of Ortiz for nearly two months, averaging exactly the same number of runs per game — 5.0 — that they had before Ortiz went down with his wrist injury may make the potential loss of Ramirez more palatable, especially if Henry has backed off from his support.

smcadam@projo.com