Are you using Forms authentication?
Forms authentication uses it own value for timeout (30 min. by default). A forms authentication timeout will send the user to the login page with the session still active. This may look like the behavior your app gives when session times out making it easy to confuse one with the other.
<system.web>
<authentication mode="Forms">
<forms timeout="50"/>
</authentication>
<sessionState timeout="60" />
</system.web>
Setting the forms timeout to something less than the session timeout can give the user a window in which to log back in without losing any session data.
I don't know about web.config or IIS. But I believe that from C# code you can do it like
Session.Timeout = 60; // 60 is number of minutes
Use the following code block in your web.config file. Here default session time out is 80 mins.
<system.web>
<sessionState mode="InProc" cookieless="false" timeout="80" />
</system.web>
Use the following link for Session Timeout with popup alert message.
Session Timeout Example
FYI:The above examples is done with devexpress popup control so you need to customize/replace devexpress popup control with normal popup control. If your using devexpress no need to customize
In my situation, it was Application Pool. It is set to restart when idle for xx mins. When I set it to not restart, it seems to use value from Web Config.
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