When you make a VPN connection your VPN connection is configured with its own IP/Mask/DNS/WINS. This is independent of your Local Area Connections.
These settings are configured on the router side.
Make sure that you WINS server is configured to point to itself for WINS resolution in its LAN connection settings.
Once that is done run NBTSTAT -RR to refresh and reload your PC's NETBIOS name cache. Then make your VPN connection and try to ping the server by name.
If all else fails search for the hidden file on your PC named "LMHOSTS". Open it with Notepad and read it. It contains instructions to manually enter the server name with its IP for proper name resolution. Make sure that you save it in the same folder you found it and delete the ".txt" file extension that will be added after you save it from Notepad.
I hope this helps.