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***UPDATE/1742 EDT***

DoD officials now say that the "manufacturing irregularities" at the Boeing plant were acts of vandalism. A reward has been offered for information in the case. Portions of the Chinook production line remain idled.

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Boeing’s chances for winning the Air Force’s next generation combat search-and-rescue (CSAR-X) helicopter contract took an unexpected hit this week, when the company was forced to temporarily shut down the Pennsylvania assembly line that would build the new rescue choppers.

As Aviation Week reports, Boeing halted production after discovering manufacturing irregularities in two Chinook helicopters being built at its Ridley Township, Pennsylvania facility. The shutdown affects CH-47 production at the plant—the same one that would build CSAR helicopters, if Boeing wins the Air Force contract.

The production pause is standard procedure in such incidents:

According to Boeing, the company notified its security organization and the site’s resident Defense Contract Management Agency representatives who oversee all U.S. government contracts at the facility. Boeing’s standard operating procedures require a thorough investigation of the incident to determine the extent of the irregularities, according to a company statement.

Subsequent reports indicate the “irregularities” consisted of severed wires on one Chinook, and a suspicious washer in the subsystem of another aircraft. The problems were discovered by Boeing employees, who conducted inspections of four other CH-47s on the assembly line. No irregularities were found in the other helicopters. Work on the helicopters was set to resume today.

Pennsylvania Congressman Joe Sestak, whose district includes the Boeing plant, said there was a “very low probability” that the damage was deliberate. “But it’s not out of the question that it’s the result of an accident,” he told Aerospace Daily. Sestak also emphasized that “the system worked” in discovering the irregularities and reporting them to the proper authorities.

But the problems at Ridley Township won’t be lost on Boeing critics—or Air Force officials still mulling the CSAR-X contract. While the brief production halt at the helicopter plant won’t scuttle Boeing’s chances of winning the Air Force contract, it will raise new questions about the company and its entry in the competition, the HH-47.

Based on the Chinook variant currently in service with U.S. special forces, the HH-47 was a relatively late addition to the initial CSAR-X competition. When Boeing won the contract in late 2006, the losing bidders (Sikorsky and Lockheed-Martin) filed a protest with the Government Accountability Office (GAO). In a rare move, the GAO upheld the protest, prompting the Air Force to re-open the competition.

A final decision on the CSAR-X contract is expected later this year. At one point, the Air Force hoped to announce the winner in early 2008, but that decision was pushed back until late summer. The delay will give the USAF more time to evaluate operating and maintenance costs for the new helicopters—sticking points in the earlier CSAR-X competition.

In the meantime, there will be whispers in the Pentagon and on Capitol Hill about the production problem in Pennsylvania, designed to raise more doubts about the HH-47. The Boeing product has its backers in Washington, but Sikorsky and Lockheed-Martin are also well-represented, and they’ll use the assembly line shut-down as one more reason to reject the HH-47.

Boeing faces the added obstacle of trying to overcome the Air Force tanker lease scandal, which sent one of its senior executives to prison, and resulted in a record, $600-million fine. While the deal was scrapped five years ago, the controversy still resonates in many political and military circles, making it more difficult for Boeing to win new, multi-billion dollar deals like CSAR-X.

At this point, the rescue helicopter competition is still a horse race. But Boeing didn’t do itself any favors, having to admit problems on its production line, in the run-up to the Air Force decision.