Start RegEdit on the SBS 2003 server.

Move to HKEY_LOCAL_MACHINE\Software\Microsoft\SmallBusinessServer\RemoteUserPortal

Modify the following DWORD values:
     For shared (public) computers - PublicTimeOut
     For private computers - TrustedTimeOut

Set the value (in decimal mode, not hex mode) to the number of minutes after which a session will timeout.

You may need to reboot the server for this to take effect.