Generally speaking, Windows will not show you shared resources on a network other than your local LAN, or allow you to contact them by name, unless you are running a WINS server in your network. However, that should not prevent you from using the IP address to contact them. I would suspect a configuration problem on your Cisco VPN appliance -- you may not have access privileges for all the Windows network service ports to the machines you are trying to reach. At a minimum, you should have TCP/UDP ports 137-139 open to those machines.
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