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Congress and the Obama administration have found a way out of the stalemate that's forced a partial shutdown of the Federal Aviation Administration. The temporary fix means a return to work for some 4,000 furloughed FAA employees, as well as an estimated 70,000 construction workers idled by the shutdown.

But as NPR's Brian Naylor reports, the underlying issues that have prevented agreement on a multi-year FAA bill remain unresolved.

BRIAN NAYLOR: The agreement was announced yesterday by Senate Majority Leader Harry Reid, who called it a bipartisan compromise between the House and the Senate. Transportation Secretary Ray LaHood told CNN last night he was happy the shutdown was about to end.

Secretary RAY LAHOOD (U.S. Department of Transportation): I'm thrilled for these hard-working people right in the middle of a construction season. They're going back to work Monday, and what they want to do: earn a good wage, take care of their families, and do construction jobs. And our FAA employees are going back to work too. I'm very, very happy.

NAYLOR: Under the deal, the Senate agreed to pass a temporary extension of the FAA's operating authority that had already been approved by the House. That House bill contains a provision many Senate Democrats objected to - one that would roll back a program that subsidizes flights to several small regional airports.

But that provision also had some wiggle room in it, language giving the Transportation secretary authority to waive the cutbacks if they were found to result in, quote, "undue difficulty" in accessing the nearest medium or large hub airport. And Transportation Department officials say LaHood will use that authority, essentially negating the cutbacks.

The waiver gives Republicans and Democrats a way out of a political mess that dimmed whatever glow Congress felt after raising the debt ceiling. The stalemate left some 74,000 government employees and contractors without paychecks, and cost the government an estimated $30 million a day in lost ticket taxes.

But while the FAA shutdown has ended for now, the underlying issues remain, which is why Congress has had to pass a series of temporary extensions rather than a long-term measure. And the biggest issue is a union dispute.

At its heart is a ruling by a rather obscure federal authority - the National Mediation Board. Last year the Board ruled that unions trying to organize airline employees would only need a majority of those voting in determining whether to unionize. That ruling reversed several decades of precedent, says Michael LeRoy, a professor of labor relations at the University of Illinois.

Professor MICHAEL LEROY (University of Illinois): Under the prior rule, which had been in existence for decades, it was necessary for a union to win a majority of all the employees in the defined bargaining unit. That meant that a nonvoter essentially voted no. That is how nonparticipation was counted.

NAYLOR: The Obama administration changed that rule so that the only votes that are counted are the votes that are cast. Republicans don't like the new rule and want to use the FAA reauthorization to overturn it.

The major airlines are all unionized, all except for Delta, where flight attendants and ground crews have been unsuccessfully trying to organize for years, says LeRoy.

Prof. LEROY: This is just the next chapter in an ongoing story about the attempt by unions to organize Delta's workforce.

NAYLOR: Democrats in the Senate, led by Transportation Committee Chairman Jay Rockefeller, are fighting the Republican effort to overturn the new ruling.

Senator JAY ROCKEFELLER (Democrat, West Virginia): Delta wants to have this law changed so that it works for their advantage.

NAYLOR: Officials at Delta would not agree to a taped interview but issued a statement, saying, quote, "Delta worked to convince Congress to reach an agreement on an extension. The labor provision is not mentioned in the FAA extension proposed by Congress."

And that's accurate. But the labor provision is part of the dispute keeping the House and Senate from agreeing on a long-term FAA authorization, and this latest agreement on a temporary extension once more puts off that day of reckoning.

Brian Naylor, NPR News, Washington.

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