Train service was back on track by 8 p.m. Monday after the storms and other problems caused rush-hour cancellations in service.
Several trains had been combined to make eastbound stops, LIRR said.
Rail road spokesman Sam Zambuto said the first set of cancellations was caused by track conditions in an Amtrak tunnel. He said he did not know the nature of the problems but that Amtrak had learned about them at 5 p.m. and was investigating.
Calls to Amtrak were not returned Monday afternoon and early evening.
The LIRR had expected a normal evening rush hour after storm-related signal problems forced a suspension of service on the Babylon and Port Jefferson branches Monday morning, and also caused scattered westbound delays systemwide of up to 20 minutes, officials said.
Service was restored at 11 a.m., and by the afternoon service on the Port Jefferson branch was on or close, according to the LIRR.
Shortly after 4 p.m., the LIRR announced the Babylon branch was also operating on or close to schedule after there were residual delays up to 60 minutes in both directions. A signal problem, at Wantagh, had been cleared, the LIRR said.
Earlier, there were scattered westbound delays of up to 20 minutes on the Ronkonkoma, Oyster Bay and Montauk branches "due to weather-related signal problems, necessitating trains to operate at a reduced speed," the LIRR said in a note to customers on its website. Those issues were resolved by late afternoon.
Railroad spokesman Sal Arena said the railroad was expected a normal evening rush hour, weather-permitting.
Even before the rush-hour deluge the LIRR already was dealing with residual westbound delays of up to 15 minutes between Mineola and Jamaica after a tractor-trailer hit an underpass near Merillon Avenue in Garden City.
That crash caused delays on the Oyster Bay, Port Jefferson and Ronkonkoma branches, the railroad said. But it was a cluster of thunderstorms that battered Nassau and Suffolk Monday morning that hit hardest.
What followed was a suspension of service on the branch. After service was restored there initially were delays of about one hour. Service also was suspended between Babylon and Jamaica on the Babylon branch, that also due to signal problems caused by the storms.
Those weather-related problems forced the cancellation of five trains, Arena said. There also were 35 delayed trains.
With John Valenti