On a warm September day at Manhattan's upscale St. Regis hotel, Microsoft chairman Bill Gates stepped onto a makeshift stage with IBM senior VP Steve Mills to demonstrate what Mills would describe as a "breakthrough" in software engineering. With the Windows operating system and Microsoft's SQL Server database running on one computer and a Linux operating system and IBM's DB2 database on another, the competitors showed how Web services could be used to conduct secure transactions across their disparate systems. It was the culmination of two years of joint effort--and ended with handshakes and smiles.

So, is Microsoft ready to ease up on its aggressive campaign to squash Linux as a competitive threat to Windows and concentrate instead on a peaceful coexistence? After all, sales of Windows and Linux servers are both growing, with many large companies deploying some of each. Have Microsoft's leaders decided it makes more sense to recognize that trend and lower the barriers to running dual platforms, rather than ignore it and keep the focus on, well, dueling platforms?

There are misperceptions when it comes to comparing Windows and Linux, Microsoft's Taylor says. Photo of Martin Taylor by Tim Jones

Don't count on it. Microsoft remains as focused as ever on beating Linux, not accommodating it. "I'm not sure what Linux-friendly means," says Martin Taylor, Microsoft's new Linux strategist, when asked if his job involves coming up with ways to make Windows a more Linux-friendly environment.

Taylor, who was previously chief of staff for Microsoft CEO Steve Ballmer, took the assignment a month after Ballmer issued a memo to employees in June that, in addition to outlining the company's business plan for the coming year, served as a call to arms against noncommercial software. "We will rise to the challenge," Ballmer wrote.

But while Microsoft works on its competitive positioning, customers are left to wrangle with heterogeneous IT environments. Despite dozens of software specs and integration tools aplenty, making Windows and Linux play together still involves roll-up-your-sleeves work. IT departments are "having to do more things manually than they should have to," says John Engates, chief technology officer of Rackspace Managed Hosting, an applications-hosting company that operates more than 9,000 servers, split almost evenly between Windows and Linux. "As the infrastructure scales up and as you support more users, it becomes more of a problem," he says.

A new survey by InformationWeek Research bears that out: Windows-Linux interoperability is an issue for more than half of the 400 business-technology professionals questioned, with 18% saying it's a significant problem. Nearly a third of respondents deal with the problem by segmenting the two environments to work independently--a less-than-ideal solution if integrated business processes are the goal.

That's just one of the challenges business technologists face when managing both Windows and Linux computers. Others include the different skills required of system administrators, incompatible applications, differing management tools, and a lack of cooperation among Microsoft and Linux vendors. Such obstacles prevent some companies from using both operating systems. "Those things are gating factors keeping us from bringing Linux in-house," says Rich Plane, chief technologist for information services at Harris Corp.

Did we say lack of cooperation? That's right. Last month's stage show notwithstanding, Windows and Linux proponents are more likely to trade barbs on any given day than shake hands at the St. Regis. And, on the matter of interoperability at least, customers pin most of the blame on Microsoft. Almost nine of 10 respondents--88%--say Microsoft hasn't done enough to support Windows-Linux interoperability. Nearly an equal number believe it will be the Linux community that works out the interoperability problems.