By Slash Lane

Published: 10:00 AM EST

In its determination to deliver the world's thinnest notebook, Apple admitted to sacrificing some speed and versatility, but a new analysis suggests that it may have given up some early profits as well.

Though the Cupertino-based Mac maker largely beat estimates for its second fiscal quarter on Wednesday, one sore spot appeared to be gross margin, which came in at about 100 to 200 basis points below most analysts' expectations at 32.9 percent.

An ensuing conference call was thus dominated by matter, as Wall Street folk routinely pelted management with questions on the perceived shortcoming as they sought a better understanding for their models going forward.

While management largely attributed the near 2 percent margin decline from the prior quarter to February's iPod shuffle price cut and a routine falloff in sales of Mac OS X Leopard and iWork, Piper Jaffray analyst Gene Munster offered his own explanation.

"We believe the margin outlook may be viewed negatively by investors, who likely wanted to see more of Apple's significant revenue upside trickle down to earnings," he wrote in a note to clients early Thursday morning. "The bottom line, we believe the margin was negativity impacted by a higher mix of Mac Book Air, which we now believe carries a lower margin."

On the bright side, Apple has likely built the potential for margin expansion into its MacBook Air design as adoption swells and component prices fall. What's more, Apple management appeared upbeat in stating that the Air has thus far shown little to no cannibalization effect on the company's other notebook offerings and thus could be considered largely responsible for helping push Mac unit growth to its highest rate in nearly two decades.

"The key takeaway from Apple's March quarter is that the Mac units grew at the highest year-over-year rates (units 51 percent and revenue 54 percent) in 17 years," Munster added in his note to clients. "Macs are the most meaningful category with the most potential and they are performing the best."

Looking ahead, the Piper Jaffray analyst said he's modeling conservatively for Mac growth rates to decline to 12 percent year-over-year for the remainder of calendar year 2008, which leaves "ample room for positive estimate revisions over the next 8 months."

"Mac growth is accelerating despite multiple quarters of strong growth, iPod sales are stabilizing with higher average-selling-prices due to the touch, and the iPhone will be significant in the second half of the year with the release of new hardware and software," he wrote.