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(The following column by L. Kim Tan appeared on the Boston Globe website on May 27.)

BOSTON — After our last column, in which we reported that the Massachusetts Bay Commuter Rail Co. was still running a peak-hour train out of Mansfield short of cars despite having been fined $1,000 a pop by the MBTA for the practice, we received mail from a reader questioning whether MBCR would pay up.

“Thanks for the comedic interlude,” wrote Rock, of Needham. “Do you know that MBCR is owned and controlled by former MBTA managers? Do you really think MBCR is going to pay a fine? Let’s print a copy of the canceled check in the Globe. Now that is really an amusing thought.”

We’ll get back to Rock’s rocket in a minute.

What we thought really amusing was, soon after receiving Rock’s note, we got word from the T saying it has fined MBCR $250,000 in the first four months of this year.

Joe Pesaturo, the T spokesman who gave us the figure in an e-mail, was not available to discuss the fines, said to be for various wrongs on the part of the commuter railroad.

But MBCR spokeswoman Tara Frier said her company is disputing many of the penalties.

Frier said the fines were imposed for shortcomings including on-time performance, consist compliance (trains short of consists, or cars), station cleaning, incident management, and employee performance (a train conductor not wearing his hat, for example). About 75 percent of the fines were for late or short trains, she said. (Those of you who ride the rush-hour commuter trains, especially the chronically crowded 7:40 a.m. express to Back Bay from Mansfield, will understand.)

MBCR was given a six-month grace period beginning last July, when it took over commuter rail operations for the T in a heralded $1 billion, five-year contract. But now the penalty clock is ticking, and the company, if not crying foul, is asking for more consideration from the MBTA and more patience from its customers.

Frier said MBCR’s problem with short trains in large part stems from aging equipment on which maintenance had been put off by Amtrak, the previous commuter rail operator. Maintenance on some of the older cars had been deferred six to eight years, she said, and getting to the work now means that some trains are going to run short of the contracted number of cars. Compounding the problem, Frier said, is having to wait on a supplier for such replacement equipment as wheels for the older-model cars.

“It’s kind of a difficult position for us to be in,” she said. “But, should we be penalized for existing conditions that we’re asked to correct?”

MBCR runs 465 trains each weekday, 172 on Saturday, and 142 on Sunday. Between 96 percent and 97 percent of the trains run “on time,” she said. The company is penalized for any train that is late by 4 minutes 59 seconds or more. Under the previous contract, the on-time threshold for Amtrak was 5 minutes, 59 seconds, according to Frier. “They had a whole extra minute,” she said. “It may not seem much, but over the course of running 465 weekday trains a day, it adds up.”

Frier said MBCR has the right to review the penalties and appeal, and it will.

“It’s not like we’re at war with the T — we’re not,” she said, acknowledging that former MBTA general manager James F. O’Leary is a partner in MBCR, an international consortium based in Boston. “We have a good working relationship — it’s just that we have to hammer this issue out with them.”

We’ll keep track of the nail.

And, to Rock: We’ll keep an eye out for that check.