NetBIOS name service is filtered by routers
I'm assuming when you say "shares" you mean samba shares. If you mean NFS or Andrew shares this answer is not applicable.
Netbios protocols don't route. The broadcasts that perform name/address translations are filtered by routers such as your GRE tunnel hosts.
Microsoft's NetBEUI gets around this with the concept of the WINS server.
You can make your samba server a WINS server but it doesn't work as automagically as you might hope...
1) Add entries to your LMHOSTS files on your clients, or
2) make your gateway hosts WINS servers (assuming they are running Samba, that is) and put entries in the LMHOSTS files on those hosts, or
3) reconfigure your tunnel to pass NetBIOS name service broadcasts.
Option 3 is the easiest but burns bandwidth unnecessarily. Option 2 is not real hard if you run your own DHCP services, because you can push the addresses of the WINS servers out to the clients when they get their DHCP leases, but if you are not running your own DHCP you have to tell all the clients where the WINS servers are so it'd be easier to just follow option 1 and put lmhosts files on the clients.
Hope this helped! I have to go to Boston for a couple of weeks so I won't be able to follow up with you any time soon.