A southbound Rail Runner commuter train was halted for about 20 minutes Wednesday night after striking a cow near San Felipe Pueblo , and morning delays from track-signal problems and missed bus connections plagued the commuter train on its first day of service between Santa Fe and Albuquerque.

Passengers onboard a train that left a station near the state Department of Transportation headquarters about 5:22 p.m. reported the train screeched to a sudden halt at about 6:10 p.m., and emergency lighting came on in passenger cars.

The conductor informed passengers over an intercom that the crew was investigating what the train had hit and later announced "everything checked out OK." The train began rolling again shortly after 6:30 p.m.

Although the train's conductor didn't disclose to passengers what the train had struck, Lawrence Rael, executive director of the Mid-Region Council of Governments, which oversees the train operation for the state, later confirmed the locomotive had hit a cow. Fences are already being installed in the area to deter livestock.

Despite the snags, many passengers remained optimistic the New Mexico Rail Runner Express would become a reliable transportation option.

"You know, they are going to have kinks, so hopefully they will get them worked out," said Marlene Benavidez, a Santa Fean who was late to her job Wednesday morning with the U.S. Postal Service in Albuquerque as a result of the train problems.

Benavidez boarded the first southbound train of the day just after 6 a.m., but that train was twice halted for longer than planned on track sidings when track-side signals malfunctioned. The train arrived in downtown Albuquerque about an hour and a half later than expected.

Meanwhile, northbound passengers on the first train into Santa Fe were on time, getting to the South Capitol station at 5:40 a.m., but those continuing their commute didn't catch a New Mexico Park and Ride bus to their jobs at Los Alamos National Laboratory. "The bus drove away as we pulled up (on the train). That ain't gonna work," Martin Nowakowski said.

The laboratory maintenance planner got on the train in Albuquerque, then ended up standing in the pre-dawn chill in Santa Fe for about a half-hour to board the next bus, along with a handful of co-workers,outside the Transportation Department headquarters. "We figured there would be hiccups along the way," Nowakowski said. "They will get it together eventually."

Park and Ride bus schedules officially change Monday to better meet trains and to eliminate redundancy, said Frank Ullom, general manager of All Aboard America, which operates the Park and Ride system. He noted the lack of overlap in this case was accidental, and the bus left at its scheduled time. Beginning today, the bus will connect with the train, even if that means waiting a few minutes, he said.

About 30 commuters rode the same train as Nowakowski north from the Duke City, with a larger number climbing aboard the next train. That train arrived about 10 minutes late into the Santa Fe Depot, and the next northbound train was delayed for 45 minutes.

Rael had hoped the first day of the train service would run more smoothly. "I'm a little frustrated and a little angry," he said in a phone interview from one of the delayed trains Monday morning. "As I walked through the train, most people said they wished it had not happened, but they understand that we are going to get better."

Aside from expecting better adherence to schedules, Rail Runner passengers are also expecting planners to come through with another promise: wireless Internet.

The state is working on a contract to get the service in place, but it's not expected until this summer, Rael said.

In the meantime, riders are making their own arrangements. Steve Cimelli, who lives in Santa Fe and works for Qwest in Albuquerque, said he's planning to get more work done on the train than on the buses he formerly used to make the commute.

"It's a longer day, but at least they have the tables and bathrooms and power," he said.

Cimelli also purchased a network card, which allows him to access the Internet without a land line.

Southbound passenger Greg Stark didn't mind the morning delays. As the sun peeked over the ridge near Waldo Canyon, where the train waited for a northbound locomotive to pass, Stark saw a rainbow in the western sky.

"I'm aware that is really special," he said, adding later, "Here we are. This train that has been shunted to the side for so many years is really here. It's a cool moment."

A midday train heading to Santa Fe carried hundreds of people, said Chris Blewett, a Mid-Region Council of Governments project manager who also rode the Rail Runner for most of the day to help with the start-up service. Final ridership numbers for Wednesday's runs will be available today, he said.

Two Santa Fe stations are now open — at the Santa Fe Depot and behind the Department of Transportation — and two others are planned, at a private development on Zia Road and on state land near the intersection of N.M. 599 and Interstate 25.

The state put up capital bonds to fund the $400 million train project, which began service in Albuquerque and Bernalillo in 2006 and expanded to Belen the next year. A portion of the money to operate the train will come from a sales tax in the seven counties that it serves.

For more information, including train schedules and fares, log on to www.nmrailrunner.com.

Staff writer Kate Nash contributed to this report.

Contact Julie Ann Grimm at 986-3017 or jgrimm@sfnewmexican.com.