NetSuite saw a 10 percent increase in revenue for the second quarter, jumping to $40.3 million this year from $36.6 million in last year’s second quarter, but the company also experienced a larger net loss on a GAAP basis.

Net loss for the second quarter was $5.0 million on a GAAP basis, or $0.08 per share, compared to $3.1 million, or $0.05 per share, in the second quarter of 2008.

However, on a non-GAAP basis, the Web-based accounting software developer performed better. Non-GAAP net income for the second quarter of 2009 was $687,000, or $0.01 per share, compared to a non-GAAP net loss of $900,000, or $0.01 per share, for the second quarter of 2008. Items presented on a non-GAAP basis excluded expenses related to stock-based compensation, the amortization of intangible assets, and transaction costs for business combinations. The company beat analysts’ expectations of $40.1 million in revenue and flat earnings.

“We were very pleased with our financial performance and strategic execution during the quarter,” said CEO Zach Nelson in a statement. “Once again, we delivered top-line and bottom-line results that exceeded expectations. We also generated operating cash in the quarter, well ahead of our plan. We remain on target to achieve our objective of posting break-even operating cash flow for 2009.” He added that the company acquired more new customers during the quarter, but did so at a higher average sales price.

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