By Calvin Biesecker

Boeing [BA] yesterday posted weak second quarter financial results, driven in part by a previously disclosed charge on an international military aircraft program but also on an unexpected dip in commercial aircraft profits as company wide sales remained flat.

The quarter “was the worst we have seen from Boeing in some time,” JP Morgan aerospace and defense analyst Joe Nadol wrote in a brief research note ahead of the company’s earnings call.

Net income fell 19 percent to $852 million, $1.16 earnings per share (EPS), from $1.1 billion ($1.35 EPS) a year ago, missing consensus estimates by six cents. Free cash was a negative $649 million. Sales were down slightly, although when rounded remained level versus a year ago at $17 billion.

The numbers stand in stark contrast to Lockheed Martin [LMT] and General Dynamics [GD], which also reported yesterday, and posted higher second quarter earnings and sales.

Still, as Boeing reported earlier this month when it announced delays in the Wedgetail airborne warning and control program for Australia would force a $248 million charge in the second quarter, the company reaffirmed its financial guidance for 2008 and 2009.

While the earnings miss was “rare,” Credit Suisse analyst Robert Spingarn said it was also “relatively insignificant” given that Boeing has maintained its earnings guidance.

In the second half of the year the product and customer mix at the commercial aircraft business will improve and the company will continue to “aggressively pursue performance improvements,” which is why guidance being maintained, Jim McNerney, Boeing’s chairman, president and CEO, said during yesterday’s earnings call.

Challenged by Jefferies and Co. analyst Howard Rubel as to why McNerney’s sustained focus on improving performance and execution didn’t seem to help the company in the second quarter, the Boeing chief said that the productivity improvements helped to “cover” the troubles in developing the 787 Dreamliner passenger plane and the Wedgetail aircraft. McNerney said he is “counting on” continued results from the process improvements to help meet year-end guidance.

Boeing’s high flying commercial aircraft business continued to accelerate production with 126 aircraft delivered in the quarter, 12 higher than a year ago, but the increased volume actually translated into less revenue. Boeing Commercial Aircraft sales declined 2 percent to $8.6 billion due to a change in customer and aircraft model mix. Boeing sees that mix shifting to be more favorable in the second half of the year, James Bell, the company’s chief financial officer, said.

Commercial operating profits tumbled 19 percent to $777 million due in part to the customer and model mix that dampened sales but also on the timing of certain expenses and infrastructure costs stemming from development delays in the 787 program. Margins declined 190 basis points to 9.1 percent.

McNerney noted that business conditions are “tough” for many of Boeing’s commercial aircraft buyers but that so far the company has seen only a “handful” of order deferrals from customers in the United States, none from elsewhere and no cancellations. However, as long as fuel prices remain high, Boeing expects additional deferrals and probably some order cancellations, all of which is normal, he said. McNerney pointed out that only 10 percent of commercial aircraft backlog is with U.S. customers and that the geographical mix of backlog around the world is dispersed such that it is protected from a downturn in one region.

Profits at the Integrated Defense Systems (IDS) Division fell 25 percent to $637 million due to the Wedgetail charge. Margins were 8 percent but absent the charge would have been 11.2 percent. Sales were relatively flat at just over $7.9 billion.

Within IDS, the Support Systems group was a bright spot, posting double-digit increases in profits and sales on its broad portfolio of services and logistics programs. Profits and sales at the Network and Space Systems group declined on lower classified work.

For the year Boeing expects sales to be between $67 billion and $68 billion and EPS between $5.70 and $5.85.

Boeing’s total backlog remained at $346 billion since the end of the first quarter. Commercial aircraft backlog under contract was up slightly from the end of the first quarter to $274.5 billion while IDS’ contractual backlog was also up slightly to $45.6 billion. Total IDS backlog was $71.3 billion.