FastCGI module available in IIS 7.0 did not work when CPULimit for the application pool was enabled. This was because when CPULimit feature was enabled WAS uses job objects to track CPU usage of worker processes. WAS keeps a job object for each application
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Read the complete post at http://blogs.iis.net/ksingla/archive/2009/07/02/getting-both-fastcgi-module-and-apppool-cpulimit-to-work.aspx