Delayed trains and other issues discouraged passengers, and traffic signals continued to puzzle drivers in Santa Fe on the second day of New Mexico Rail Runner Express service to the city.

Malfunctioning track-side signals slowed down trains Thursday morning, and that — coupled with delays they experienced the day before — caused some commuters to leave train stations in their cars and use the interstate instead.

Among them was Gary Smith, who took a car full of would-be train riders with him.

"I was an hour late for work yesterday, ... and I was on the train that hit the cow last night. And then this morning, they were 30 minutes late," Smith said Thursday. "So myself and some other people got in my car, and we saw numerous other people leaving."

Train planners say delays have plagued the opening days of service in an unexpected way, emerging both from older track-side signals just north of Albuquerque and from software that runs new signals on fresh tracks laid this year on the approach to Santa Fe.

"We have to continue to do the best we can to isolate these problems," said Chris Blewett, project manager for the state's train planners at the Mid-Region Council of Governments.

"Yesterday and today, we have had a run of problems that we have not experienced before in terms of the severity," he said Thursday. "We have a lot of people working on this, ... and we believe we have got (the problems) addressed."

For Smith, the delays became unacceptable. "If the train is not ready, then they need to shut it down and get things fixed so it ready to go," he said. "For trains to come in late like this and take so long, that effects people's jobs."

Others had concerns that one of Santa Fe's two open train platforms has not been completed. Santa Fe resident Sig Rivera was planning buy his commuting daughter a flashlight and mace Thursday because the lights at the South Capitol station platform were not turned on the night before.

"They were in pitch black last night, so that kind of worries me," he said, noting his 22-year-old-daughter works until 6 p.m. and will frequently catch the train in the evening.

"Anything can happen in the dark. ... You'd think the lights would be on right away before they started to make sure they work right and illuminate the area," he said. "They are in too much of a hurry."

Blewett said lights were expected to be on soon.

"We just got the power pole in on Saturday, and we had to run a pretty long length of electrical conduit to it, and with the weather, we didn't get it done on time," he said.

Wet winter weather has also slowed the application of final road striping at intersections where the train crosses Santa Fe roadways, said Blewett.

Although temporary striping and permanent signage is already in place, drivers have been both frustrated and panicked as they interact with gates and flashing lights.

"People are still pulling up past the gates, and the gates are coming down on top of cars. That is probably the biggest thing we are seeing now," Rick Devine, a city traffic engineer who sent workers to observe signals at each intersection. "I think driver behavior will change as they get used to all these trains coming through. It takes time to change behavior."

Devine said traffic is not backing up like he expected at train crossings, and the signals don't appear to be out of sync because of them. "The queues were fairly reasonable, so it may not be as big an impact as we initially thought. So far, so good," he said.

City police have issued about 20 warning citations to drivers who stop in dangerous areas at train crossings, said Deputy Chief Benjie Montaño. Beginning next week, traffic patrol officers will "really start hitting it hard," he added.

Another issue reported by drivers is from gates that come down and stay down, even when no train appears in the intersection. Driver Carol Kelly said that happened Wednesday night at the intersection of Cerrillos Road and St. Francis Drive.

Blewett said this phenomenon occurs sometimes because of train movements in places like the Santa Fe Railyard, where Santa Fe Southern excursion trains are restaging and moving around. Signals work on circuit blocks, so when a train gets within a block that controls an intersection, the warning signals will engage, he said.

"Just because you can't see a train, that does not mean there is not one there. The circuits that trigger those gates are pretty far off," he said.

Kelley said she has made a special effort to stay behind the white lines painted at intersections, but she's seen a lot of other drivers disobey the stripping. "It seems like people just ignore it," she said. "They are so used to going right out there."

Ridership reports for Monday indicate 2,900 train trips, with most originating in and around Albuquerque. About half the riders got on at the N.M. 550 station and another 20 percent boarded at the Albuquerque Journal Center. Trains are free to Santa Fe County residents for the first three months of operation.

For more information about train schedules or fares, log on to www.nmrailrunner.org or call 1-866-795-7245.

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