I had similar problems with timeouts on PHP, but I am using IIS 7.0 which doesn't have a fcgiext.ini. It turns out that the FastCGI configuration is now in main IIS XML configuration, modifying fcgiext.ini would make no difference.
Here is how to set the configuration with IIS 7.0:
%windir%\system32\inetsrv\appcmd set config -section:system.webServer/fastCgi /[fullPath='C:\php\php-cgi.exe'].activityTimeout:600
You need to change the 'C:\php\php-cgi.exe' to the actual location PHP that you registered with IIS.
If you want to make double-check that the configuration worked properly, you can check it like this:
%windir%\system32\inetsrv\appcmd list config -section:system.webServer/fastCgi
You should see output similar to the following:
<system.webServer>
<fastCgi>
<application fullPath="C:\php\php-cgi.exe" activityTimeout="600">
<environmentVariables>
</environmentVariables>
</application>
</fastCgi>
</system.webServer>