Netbooks are becoming an unexpected problem for Microsoft, according to Bloomberg. Acer Inc. and Asustek Computer, two of the big names in the netbook market, who make up 90% of said market, are using Linux on about 30% of their netbooks. Of course, Linux has always been a fairly non-threatening rival for Microsoft’s Windows series, but with the increased usage of it on netbooks, Microsoft are surely starting to get worried.

The article cites netbooks as the fastest-growing segment in the PC industry and claims that their emergence is eating into Microsoft’s profits. Windows sales fell short of forecasts in the last quarter, causing Microsoft to cut growth projections, and actually admit that netbooks are the main cause for this. Netbook manufacturers who do use Windows – still 70% of models (but significantly lower than the 90% of PCs that also use it) – tend to use old versions of the operating system.

Microsoft is taking this seriously and is already taking steps to ensure it is ready for the netbook boom. Windows 7, the scheduled successor of Windows Vista, will work much better with netbooks according to Senior Vice President Jon DeVaan. DeVaan said, “People will be pleasantly surprised and excited” by how Windows 7 runs on low-cost machines. We’ll do well on those kinds of machines.”

Despite Microsoft’s initiative to stop this growing problem, Bloomberg claims that Windows will still be a tough sell for PC makers trying to develop the cheapest machines possible. Jenny Lai, a Taipei-based analyst at CLSA Ltd., says that Linux costs just $5 to put on computers, compared to with $40 to $50 for XP and about $100 for Vista, a huge difference.