National Transportation Safety Board member Debbie Hersman told a House subcommittee that investigators are replacing various pieces of equipment in an attempt to stop the problem from occurring on a portion of the red line near the Maryland border.
So far, she said, nothing has worked.
"It's a mystery as to what's going on here," Metro board chairman Jim Graham told lawmakers.
Nine people were killed and more than 70 injured June 22 when a Metro train slammed into another train stopped on the tracks.
Metro's signaling system is designed to prevent crashes by generating speed commands and not allowing more than one train to occupy a section of track. But problems began occurring after a piece of equipment was replaced five days before the crash.
Investigators are continuing to examine how the system was functioning at the time of the accident. If the system was malfunctioning, the oncoming train could have lacked information that another train was stopped on the tracks.
Investigators have said there is evidence the operator of the train that was moving, Jeanice McMillan, applied the emergency brake before the crash.
McMillan was among those killed in the accident.
Metro General Manager John Catoe said Tuesday that trains continue to run manually systemwide until the cause of the crash is determined. Added precautions are being taken near Fort Totten, where the crash occurred.
"Operators have to go at slower speeds and need permission from the radio control center to proceed," Catoe told reporters. He said that is causing ongoing delays on the red line, and he asked passengers for patience.
Tuesday's hearing was held one day after the NTSB urged Metro to upgrade its signaling system with continuous backup protections. Investigators want Metro to evaluate the system in real time so that the operations control center is immediately alerted about a problem. Trains would then be stopped or slowed to prevent a crash.
"You've got to get an alert when something fails," Hersman said. "We want to make sure that when the system isn't functioning as it was intended, there's some way to find out about it so we can intervene."
Metro officials planned to meet Wednesday with vendors for help developing such a system, Catoe said. For now, Metro says it is only able to review data once a day to determine whether the system is functioning properly.
At the NTSB's request, the Federal Transit Administration has sent a letter to transit systems nationwide asking that the agencies also make sure they have adequate backup protections in case their train control systems fail.
The American Public Transportation Association says technology similar to Metro's is used in other big cities, such as Atlanta, Baltimore, Boston, Miami, Philadelphia and San Francisco.