Neither transportation officials nor the region’s thousands of commuters really expected the Massachusetts Bay Transportation Authority’s switch to new train schedules to go absolutely perfectly Monday.

The T changed the schedules for nine of its 12 commuter rail lines to ensure more on-time trains, yet only 85 percent of the morning trains arrived on time. Two Lowell trains were delayed in the morning by more than half an hour because of problems with a signal. Some customers on the Stoughton line noticed their rides were a bit more crowded than usual. And the commuter rail’s newest service, an express trip from Worcester to Boston, came into South Station four minutes late on its inaugural run because people were busy getting off at Yawkey Station and snapping photos.

But to hear many people tell it, Monday didn’t go too badly.

“I feel like for the first day of a schedule where we changed a lot of people’s trains, it’s been a good commute,’’ Transportation Secretary Stephanie Pollack said Monday morning. “Services are running on time; people seem to be finding their way to their new trains.’’

At Swampscott’s commuter rail station, Shan Franklin of Marblehead said he had been aware of the changes because Keolis employees had been passing out schedules at North Station for weeks. Franklin used to take the 6:49 a.m. train from Swampscott into Boston, but the new schedules took away that option. Unfortunately, he didn’t remember.

“Everybody knew about the new schedules because they’ve been handing out schedules,’’ Franklin said. “Of course, I still forgot about it.’’

Meanwhile, Alice Cabotaje of Swampscott hadn’t gotten the message at all. She was out of town all last week, so she didn’t get one of the 87,000 paper schedules handed out. When she arrived around 6:40 a.m. at Swampscott, she realized she had just missed the new 6:36 a.m. train and would have to wait for the new 7:05 a.m. train instead.

She lamented the loss of the 6:49 a.m. train; it wasn’t as crowded as the trains right before and right afterward, and got her into work at just the right time.

“I’m disappointed, because it reduces flexibility,’’ she said.

MBTA officials say that being on time was the primary goal behind the new timetables. If a train was consistently late according to the previous schedule, officials changed travel times to reflect how long the train trip actually took. Perhaps more important, they also built in more time for trains to change directions at the end of the line. That way, officials say, if a train gets delayed, it doesn’t make every other train behind it late, too.

On Monday, there were still some delays. Sakal Kim took the new 6:57 a.m. train from Lowell. The train eventually got delayed because of a problem with a signal.

Kim finally got into North Station around 8:25 a.m., more than half an hour later than scheduled.

“I hope tomorrow is better than today,’’ he said, as he speed-walked across the street to take the Orange Line.

The new schedules did make some people happy. Delia O’Connor called the commute “smooth’’ after she rode on the first “Heart to Hub’’ express train from Worcester to Boston, which stops at the Yawkey and Back Bay Stations before finally ending at South Station.

A Worcester to South Station train that makes all of its 16 stops usually takes more than 90 minutes, but the new express line goes from Worcester to South Station in a little more than an hour.

On that first ride, O’Connor was joined by Pollack, Lieutenant Governor Karyn Polito, MBTA chief administrator Brian Shortsleeve, and Congressman Jim McGovern.

The train rolled in at about 9:11 a.m., about 4 minutes after it was scheduled to come in. Under MBTA rules, that doesn’t actually count as a late train; only trains that are more than five minutes late get that designation.

At a ceremony held at South Station afterward, Polito said the new train — and its evening counterpart, which leaves South Station at 7:35 p.m. — is transformational.

“I view this as two major things: It’s economic development,’’ she said, adding it could bring more jobs and opportunities to Worcester, and allow Worcester residents more options for the commute. “It’s also a development in terms of lifestyle. . . . We’re able to promote Worcester as a viable option for young people who are very much a part of our innovation economy.’’

Commuters such as O’Connor found a much simpler bright side, though. Even if the train is four or five minutes late, O’Connor said it’s still better than waiting on the older version of the train.

“It gives me 40 minutes back,’’ she said.

Nicole Dungca can be reached at nicole.dungca@globe.com.