The contract includes the installation of positive train control hardware on 32 MARC locomotives and 30 cab cars, as well as maintenance of the equipment through 2017.
However, Amtrak uses a different system.
Hovatter said the systems are compatible on trains traveling as fast as 79 mph, but some MARC trains reach 125 mph — and compatibility is an unknown at those speeds.
To address that issue, Amtrak and MARC plan to build a "test bed" of tracks north of Perryville in coming months to test compatibility at higher speeds, under a $700,000 grant from the Federal Railroad Administration, Hovatter said.
While a lot must still be worked out, the outcome — increased safety — will be worth it, he said.
The NTSB has been advocating for the implementation of positive train control since at least 1990.
The Brotherhood of Locomotive Engineers and Trainmen, which represents 51,000 engineers and trainmen across the country, said it "provides a safety overlay that assists locomotive engineers as they approach speed restrictions as well as required stops."
However, advocates of the technology have long butted heads with railroad industry leaders concerned about the costs and logistics involved in implementing the systems.
While almost all railroads are implementing the systems now, most will not finish by the deadline, citing billion-dollar price tags and issues with securing required radio bandwidth, according to a U.S. Government Accountability Office report from August.
Issues of interoperability — like those facing MARC — are also high on the list of problems, as is the pace at which the technology is advancing ahead of the deadline, according to the report.
"Most railroads report they will not complete PTC implementation by the 2015 deadline due to a number of complex and interrelated challenges," the GAO report found. "Many PTC components continue to be in various stages of development, and in order to ensure successful integration of these components, railroads must conduct multiple phases of testing before components are installed across the network."
"All the technology stuff, that's the big problem," Hovatter said. "That has been the big bugaboo from the beginning."
CSX's Lewis said there was also the fear that early system problems, unaddressed amid the time crunch, could have a major economic impact.
"If it works the way it's designed, it's a good thing," he said. "But if it stops trains when it's not supposed to stop trains, it's obviously very bad for business."
The Federal Railroad Administration has requested the authority to extend the deadline on certain rail lines — a request the GAO report endorsed. A handful of U.S. senators have introduced legislation to delay the deadline.
Still, most rail operators are pushing ahead as fast as possible, officials said.
"It's going to make things safer," Hovatter said. "It's been proven to do that."