Hello Mark,
Never used the Factory Configuration.
To control the session timeout on an application, we just create a simple extension with a method to set the session timeout, and use this inside it:
HttpContext.Current.Session.Timeout = ssMinutes;
HttpContext comes from the System.Web
As you can see, we are dealing with .NET only here.
Maybe this can be useful, if you also are using .NET and are not using other settings from Factory Configuration.
Cheers.