Are the users getting the popup message that
says:
Idle timer expired : Session has been idle over its time limit.
It will be disconnected in 2 minutes.
Press any key now to continue session.
If so then the idle timeout is set somewhere else.
Session timeouts can be set:
On the Connection object
Start–>Run–>tscc.msc–>right-click RDP-Tcp–>Properties–>Sessions tab
On the User object
Active Directory Users & Comp–>right-click the user–>Properties–>Sessions tab
On the Group Policy object
Edit the GPO–>User–>Admin–>Win Comp–>Term Serv–>Sessions
And
Edit the GPO–>Comp–>Admin–>Win Comp–>Term Serv–>Sessions
The users may not have noticed the popup window, so
check the event log for Application Popup entries.