My experience with the Cisco VPN client is only a few days old, so my help is minimal, but it's offered nonetheless.
nuggetman: can you use your VPN via the VPN option in the Internet Connect program in your /Applications folder?
No, he can't. This is because the Cisco VPN client is used when a business makes the (bad) decision to use their Cisco box as a concentrator / VPN gateway, and this is (bad) proprietary. It doesn't support the standard VPN flavor.
I don't do Windows, but I can suggest that you debug the problem this way:
(1) At the office figure out a script of things (both vanilla TCP/IP and Windows actions) which work. For example, use your web browser to see the company's employee directory, ping the internal build machine or IT's patch server, etc. Mounth that SAMBA drive, etc. Write down exactly what you've done.
(2) At home, with the Cisco VPN client *off* verifiy that all this fails.
(3) With the client *on* try the TCP/IP stuff first. They ought to work if the Cisco box is properly configured and you're actually corrected. Then try the windows things which worked. Do they still fail? In what way(s)? Tell your IT guys or us. Details count.
Good luck. I feel your pain.