I don't have a scientific answer but after I started hearing about it and made some excursions out to DIA it was mostly losing time at stops by forgetting to make announcements, overly long stops, misjudging their speed into the phase break outside of Union Station, and yes, underspeed perhaps as a way of avoiding PTC violations. There is lots of single track in the system and the schedule adherence of everyone is critical.I'm curious as to why.
Did they just like to run below the speed limit? Were they overly cautious about curves & switches? Chronically late for work?
When the schedules were being worked out with the contractor, they initially tried to have adherence measured like the bogus method used by Eastern commuter railroads (logging the time at terminals). Perhaps they thought we'd be impressed. Our light rail and buses are measured at every time point by German technology. The non-CBD riders transferring with bus or other rail lines deserve reliable service, not just the passengers going in and out of Union Station.
Subsequently things have gotten better, but I do know that some of their operators went back to freight railroading in spite of its unpredictable, weird hours and other burdens.