You're correct that the clock starts ticking as soon as you login to the Connection Server but only for the client connection itself. The session on the desktop itself is independent of this clock and is not affected directly.
The setting that you want to use to control this more tightly is the "Automatically logoff after" option in the desktop pool settings. This setting allows you to set various policies based on the type of pool the user is using.
For example, if you have a Floating pool used for task access with no requirement for persistence across sessions on the desktop itself you can set this setting to immediately. As soon as the client disconnects the desktop will be reset. Alternatively you can set the "After..." option to a small period of time, like 5-60 minutes. This allows the user to disconnect for a short period of time, such as a lunch or coffee break but still be able to log back in and continue on with their session, but the desktop will be logged off at the end of the day or into the evening once the session timeout is hit (if they leave the client logged in when thy go home).
Another common scenario is to have the logoff after disconnect option set to something like 17-18 hours. This allows a user to have a persistent session through the week so they get a consistent experience. It also means that each weekend, when the user isn't logging in within 18 hours the desktop will logoff and be released back into the pool.
If you need some amount of persistence but a hard timeout on a Windows session itself this would need to be handled by a 3rd-party utility inside the OS itself.
Hopefully this is helpful!
-Mike
Twitter: @MikeBarnett_
