What about HTTP request timeout? (By Web.config, I think you must have just tried session timeout and not httpruntime)
<httpruntime enable="true" maxrequestlength="10240" executiontimeout="360" />
Checkout following blog entry: Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding.
Further, you sure it's not commandtimeout? (default 30 sec)