In a recent post to his IIS.net blog Don Raman wants to help out all of those developers getting timeout messages on their PHP scripts running on a Windows platform and how some FastCGI settings could help.

Let's try to understand the reason behind this. [...] Let me now summarize some of the IIS FastCGI settings and PHP INI configuration directive to ensure that everyone is on the same page and which are most important for this discussion.

The two FastCGI settings he mentions are the ActivityTimeout and the RequestTimeout as well as a generic PHP setting that could be a cause of the problem, max_execution_time. He suggests some default values for each of these, but only experimentation will help you find the right balance of these three. It's a great starting place to look, though - especially if you've been battling the problem for a while.