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Rebooking delays extended by packed planes

Frustrated air travelers are caught in a series of storms that have canceled thousands of flights and stranded people as planes were already so full they don't have enough empty seats to get everyone home before the next round hits.

'It's the rat-a-tat, one after another," said George Hobica, the founder of AirFareWatchDog.com. "It's a cumulative effect."

The latest storm caused JetBlue on Monday to announce a phased-in shutdown of its operations in Boston and New York.

Daniel Baker, the CEO of FlightAware, said the extreme cold wave hitting Monday would not be out of the ordinary on its own.

"This is winter in the Northeast. This is not an exceptional storm," he told CNBC.com on Monday morning before JetBlue announced its shutdown decision. "Some things are different in that a lot of it is temperature driven and less snow accumulation. Also Chicago has been hit twice. They're by far the worst, with over 60 percent cancellations."

The Flight Aware misery map also shows significant delays in New York, Cleveland, Washington, D.C. and elsewhere.

Another key factor to the rebooking delays is that year-round, airlines have refined their businesses so that they are flying with fewer empty seats.

"There's no question that's the case, the load factor has increased on these flights so when there is a disruption there is less space to replace them," Baker said.

(Read more: Cuts in air service stifling midsize cities)

JetBlue also cited new pilot-fatigue rules adopted over the weekend that require the people flying the plane have enough time to rest between flights..

"The new year began with the winter storm some called Hercules, is shutting down the heaviest trafficked air corridor in the world during one of the heaviest travel periods of the year. Mother Nature then followed that up with icing conditions over the weekend, causing even more issues and ground stops at the airports. Even as airports began to reopen though, newly launched FAA regulations on pilot duty times caused delayed flights to quickly turn into canceled ones. Now today, less than a week into the year, we're watching a polar vortex wreak havoc on flight schedules across the industry, as rainy weather prepares to turn airports in the Northeast into ice rinks once again," the company said on its website.

The good news, Baker said, is that airlines are making changes early and travelers have more information than they did even five years ago when they were more likely to show up at the airport only to learn they had few options.

"It's smart for people to be proactive. You can take advantage of all that information only if you're paying attention. If you're flying, pay attention a day in advance. You can reroute now," he said.

(Read more: On jammed jets, sardines turn on one another)

Hobica agreed, and advised passengers to call their airline well in advance and ask for a direct flight around an approaching storm, even if they bought a nonrefundable, nonchangeable ticket.

"A lot of people think they're stuck with what they bought," he said, but it's fairly common the airline will make the change for free if they can find a seat on another plane in order to get a traveler away from a major storm facing cancellations.

Thousands of people with delayed or canceled flights waiting in the customer service line at O'Hare.
Phil Lebeau | CNBC
Thousands of people with delayed or canceled flights waiting in the customer service line at O'Hare.

And while the airlines are under no obligation to pay for hotels if the weather caused the cancellation, "they might do it for their best customers," he said. Otherwise, stranded travelers will be left to fend for themselves finding a hotel or the pajama party at the airport.

—By CNBC's Amy Langfield. Follow her on Twitter at @AmyLangfield.

Follow Road Warrior on Twitter at @CNBCtravel.

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