A commuter uses a ticket machine at the LIRR station...

A commuter uses a ticket machine at the LIRR station in Valley Stream. Credit: Ed Betz, 2011

Yesterday at Penn Station: Passengers are boarding a Long Island Rail Road train to Huntington. Suddenly, through the open train doors, comes the indistinct din of a complicated public address message. A rider says it's a track change. Then over the PA system comes a barely audible track number. Some riders stay seated. Others go to the new track. But the empty train on the new track doesn't open its doors. Some stand around on the platform. Others filter away. The LIRR offers not a clue. There are no employees to ask. At last, the PA announces a power problem. Nobody's going anywhere. Riders groan and curse.

While the delay was short-lived, maybe 20 minutes in all, it wasn't the best way to get LIRR riders into the mood for the fare hike -- averaging a painful 9 percent -- that starts tomorrow.

The truth is, the Metropolitan Transportation Authority -- owner and operator of the Long Island Rail Road and the New York City subway and bus system, among other things -- is rolling through rough times. Money is tight, revenues are uncertain, contract talks are stalled, and the agency's top job is up for grabs. As fares climb, service -- while better -- isn't what it should be.

With a very thin margin for error, the MTA must get its act together.

It didn't help recently when State Comptroller Thomas DiNapoli released a stinging audit that said the MTA let $92 million sit idle in bank accounts instead of using it to pay expenses or to boost MTA investments.

The MTA disputes DiNapoli's report vigorously and in detail. But the damage is done. Rider advocates see the $92-million figure and imagine service cuts that might have been prevented. Union leaders see it and dream of fatter contracts.

As for the LIRR, it did win high marks for its overall performance in the weekend snowstorm that started Feb. 8. But while the railroad did many things right, familiar difficulties remain. On the plus side, LIRR president Helena Williams' new emergency control center in Jamaica worked well. Dozens of employees sitting side by side kept an eye on the weather and monitored 700 miles of track. As soon as 10 inches of snow accumulated on the rails, the railroad shut down service.

As a result, no passenger-filled trains bogged down between stations. New equipment helped keep tracks clear during the storm, and the Feb. 11 morning rush opened with only minimal difficulties.

Yet communications remain a problem. Yesterday's confusion at Penn is one example. Here's another: When high winds knocked down a utility pole near Hicksville on Jan. 31, causing service disruptions, a familiar cycle of cancellations, delays and conflicting information quickly infuriated riders. The LIRR must get this right.

Meanwhile, the MTA urgently needs a permanent leader. It has been without one since Joseph Lhota quit as executive director at the end of 2012 to run for mayor of New York.

While interim executive director Thomas Prendergast has delivered a strong performance running the largest transportation system in North America, Gov. Andrew M. Cuomo should make the MTA appointment a priority. And then? New contracts with transit system workers -- signed and sealed -- would be nice. So would better communications. And so would budgets that don't take such a nasty bite out of riders' pocketbooks as the MTA rumbles into the future.