I ran into this trying to upload 20 meg files. It would timeout after 3 minutes or so no matter what. I checked everything in iis, php.ini, and in the script. Finally a person by the name of michael defrees showed me what was wrong. It is an IIS issue, there is a timeout in a weird place in addition to the normal "connection timeout" setting under the 'web site' tab.
To fix go to 'www root properties'
then 'home directory' tab
click on 'configuration' (bottom right)
This gives you the 'app mappings'
click on the 'Process Options' tab
then you'll see the setting for CGI script timeout for what you want.
