For its full fiscal year, Red Hat now sees earnings of $1.07 to $1.08 a share. The average analysts' view is for profit of $1.05 a share.

Whitehurst said Red Hat was "scratching their heads" when looking at the market reaction -- the stock fell 8% in after-hours trading Monday night, and the selloff continued Tuesday, down 9.3% to $41.74.

"We're pretty happy with the result, the performance was extremely strong," he said.

Shares are down 7.7% year to date.

Whitehurst was very positive on Red Hat's $136 million acquisition of cloud storage company Gluster. "We think it Gluster is really the only good solution for cloud storage," he said.

Gluster is different from other data solutions in that it does so in a low cost, open source manner. He noted that operating margins will be hit in 2012 as the company invests in Gluster, but he thinks the acquisition will be accretive in the long run.

When asked about Europe, Whitehurst said "the pipeline looks strong," and that he had not seen a lot of headwinds out of the region. He did note that southern Europe is a bit more challenged than northern or central Europe.

-- Written by Chris Ciaccia in New York

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