Can the prolonged delays and ongoing difficulties in opening and operating the metro area’s commuter rail system — not to mention the millions of dollars assessed in penalties and spent on flaggers over the last two-plus years — be traced to the issue of bicycle safety?

That’s what the private sector consortium that was hired to build and run the University of Colorado A-Line, G-Line and B-Line is asserting in a lawsuit filed last week in Denver District Court against the Regional Transportation District.

Denver Transit Partners claims that in the summer of 2015 — nearly a year before the A-Line opened passenger service — a staff member with the Colorado Public Utilities Commission expressed concern that cyclists might find the safety-equipped crossings “confusing” to traverse.

That led to RTD, over the consortium’s objections, requiring “exit gate delay” technology at crossings that would have the ability to detect bicycles, even though no such technology existed or had been approved by federal railroad regulators, the lawsuit maintains.

What followed, according to DTP, was a cascading series of reviews, demands and delays from state and federal regulators that continue to reverberate today, with the G-Line’s launch nearly two years past due and round-the-clock blasts from train horns still shaking residents awake from Aurora to Wheat Ridge as implementation of quiet zones remains stalled.

“Amending the original design applications had the effect of reopening the entire design process and exposing the project to additional notice and comment periods that jeopardized the opening of the A-Line and, as would be seen, resulted in additional delays from unprecedented actions by (the PUC) and the (Federal Railroad Administration),” the lawsuit says.

The $2.2 billion contract the consortium signed with RTD in 2010 never spoke to the need for bicycle detection at crossings, DTP argued, and amounted to a “change in law” against which the consortium is legally protected. It said the PUC staffer’s “insistence that an exit gate delay be employed at the project was based upon misinterpretation of Colorado traffic law, which provides that bicyclists must obey traffic rules.”

Just a few months later, regulators introduced a “new and unprecedented requirement” for DTP to meet, according to the suit — an order to fix allegedly inconsistent and excessive warning times at the crossings.

This re-examination of the system’s design, prompted originally by concern over cyclist safety, “was a producing cause of and contributed to a two-plus year delay for DTP, and subsequently exposed DTP to millions of dollars in unanticipated costs …,” according to the suit.

DTP wants to be reimbursed for the cost of paying crossing attendants on the A-Line and G-Line for the last two years, a dollar amount it did not specify in its suit. It also slammed RTD for docking it $250,000 a month in penalties — for a total of $6 million that it also wants back — when the A-Line has been operating as it was designed to do.

DTP said RTD “had no urgency surrounding the removal of the crossing guards,” given that the penalties DTP was paying were to the “benefit of (RTD’s) own budget.”

A DTP spokeswoman referred further questions to the consortium’s complaint. A spokesman for the PUC declined to comment, saying it is not a party to the lawsuit.

RTD spokeswoman Laurie Huff on Tuesday told The Denver Post that the transit agency disagrees with the claims in DTP’s lawsuit and will likely file a response in court in the coming weeks.

“The companies that make up DTP have not accepted responsibility for their project and are trying to blame others,” Huff said. “RTD has been discouraged by DTP’s delay in satisfying its obligations.”

The companies in the consortium include heavy-hitting engineering, construction and investment firms Fluor Corp., John Laing Group, Aberdeen Infrastructure Investments, Balfour Beatty Rail, and Ames Construction. The contract for the three lines, known as the Eagle P3 project, is considered the first public-private partnership on construction of a commuter rail system in the United States.

The 23-mile A-Line, which opened in April 2016, ran into immediate challenges when it was halted by lightning strikes and other unexpected delays. Many of those issues have since been resolved.

G-Line service, which runs 11 miles through Adams County, Arvada and Wheat Ridge, remains idled even though the track and stations were completed years ago. Its launch has been delayed by ongoing problems with gate timing issues on the A-Line, which uses the same technology at its crossings.

This past summer, it looked like the project was on the upswing when regulators allowed RTD to dismiss crossing guards on the A-Line, a necessary step before quiet zone applications can be filed. But last month, a test train on the G-Line reached a crossing ahead of the safety gates’ minimum 20-second warning time.

The incident triggered the Federal Railroad Administration to order reinstatement of flaggers at three A-Line crossings and the lone crossing on the B-Line, which serves Westminster. It’s not clear when those flaggers will be allowed to step down again.

Huff said RTD is “very disappointed at how long DTP has taken to get the G-Line ready to open.”

“RTD regrets that its constituents are still waiting for stations to open and still waiting for the horns to stop,” she said.