The MTR East Rail service came to a complete halt for the second day in a row yesterday amid further problems with the system showing the trains' location.
Railway managers stopped the service in the morning rush hour after "flashes" in the backup monitoring system - in use since Sunday's incident - froze images on the screens.
The seven-minute stoppage, though shorter than Sunday's half-hour shutdown, still sparked anger among passengers.
"[The MTR] said 'Please forgive us'. I'm absolutely not forgiving them," one man said.
It also brought an accusation of negligence from Michael Tien Puk-sun, chairman of the Legislative Council's railways subcommittee. Tien said the MTR had failed to do regular test runs on its backup system.
"If your backup system doesn't work when you need it, it's useless," he said. "You need to do test runs from time to time to see whether the backup will switch on automatically when the system fails."
An MTR spokesman said the service resumed after the system was "restored" and an investigation was under way to find out what had caused the problem.
General manager for infrastructure Terry Wong Wing-kin admitted no test runs were conducted on the backup system to ensure it would start automatically when the data network system was checked in December.
The backup had to be started manually on Sunday morning, which lengthened the service suspension to 36 minutes.
Wong confirmed that there had been three "screen flashes" since the backup system came into use, two on Sunday - which may have caused some train delays - and one yesterday.
During yesterday's disruption, Fanling station had to be closed after 7.40am due to overcrowding. It reopened at 8am.
Wong, who apologised on Sunday, did so again yesterday.
He said the railway was still investigating whether the failures were related and their exact causes. A defective router was replaced on Sunday night.
The MTR has asked the Australian supplier of its data networking system to send staff to Hong Kong to help in the investigation, Wong said.
But the news was no comfort to one of the frustrated passengers affected by yesterday's disruption.
"It just broke down yesterday, then today, there's this ... I came in and can only wait," she said.