So, you are running the server in one subnet and all clients in the second subnet.. First, 2008, I believe, installs with the Computer Browser Service turned off, so check that..
Regarding using Netbios across subnets? You need a Domain Master Browser in both subnets.. Might want to quickly read my page on Netbios here:
http://65.24.164.204/KipSolutions/NetBios/netbios.htm