If I recall correctly, netconfig, will configure /etc/HOSTNAME, /etc/resolv.conf, /etc/rc.d/rc.inet1, and I think also /etc/rc.d/rc.netdevices if a module is required. But it doesn't actually execute anything. That would be on the next reboot it should load through the init scripts.
But it is required to have a net card identified and loaded either by kernel or module before ifconfig can to do anything on eth0 or eth1. If your net card module is loading AFTER rc.inet1 runs then it wasn't present when it was configured. If ifconfig output is missing eth0 after reboot, then it is not loaded properly.
What model are your two NICs?
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