A new lawsuit from RTD is revealing serious problems with the A Line before it opened in 2016. The A Line is the commuter train that runs between Union Station and DIA.

The suit is in response to one from RTD's partner on the commuter rail, Denver Transit Partners, which sued RTD in September for $6 million the group says RTD is withholding from them.

DTP built the rail line and operates it, along with the B Line to Westminster and the as-yet unopened G Line to Arvada and Wheat Ridge.

The RTD lawsuit accuses DTP of building rail bridges for the A Line incorrectly, claiming some bridges had to be retrofitted or rebuilt altogether. It goes on to say the replacement bridges are still not up to standards and will lead to higher maintenance costs for RTD.

Also detailed in the lawsuit: a near-collision between a train and two vehicles at a crossing just a few weeks before trains began taking passengers in the spring of 2016.

RTD also faults DTP for ongoing problems with the A Line, as well as issues that have kept the G Line from opening two years past its scheduled start date.

Because of the troubles with DTP, none of the lines have achieved "Quiet Zone" status as required per the pair's contract, RTD's claim says. So trains must continue to blow their horns at every crossing.

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"Although the A Line and B Line opened on time, they did so with deficient and incomplete systems," the suit continues. RTD also references their troubles with the Federal Railroad Administration and the Colorado Public Utilities Commission - namely that those organizations required flaggers and other crossing guards because of the Transit Partners' poor performance on safety and subpar grade crossing activation system.

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Denver Transit Partners says in its suit against RTD that the agency is withholding money for services rendered. RTD says the group is shifting the blame to regulators and RTD themselves, per their court filing.

"With all due respect, RTD thinks DTP should be looking within, rather than trying to blame safety regulators, for the challenges DTP has faced," RTD said in a statement to 9NEWS back in September.

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For RTD, the dispute boils down to DTP agreeing to take on the designing, building, financing, operating and maintenance costs of the rail line, per their contract. For DTP, the costs of running the trains have skyrocketed due to undue scrutiny from state and federal agencies, something they don't believe they should be on the hook for. They want the $6 million they say RTD is withholding from them.

Negotiations had been underway for months prior to Denver Transit Partner's court filing but broke down in September.

In their counterclaim, RTD says they'd like an unspecified amount of damages to be awarded to them at trial for the Transit Partners' alleged breach of contract.

The full list of counterclaims can be viewed below or at this link.