Are you sure the missing one is the old one? If one of your two NICs isn't detected the remaining one is always eth0.
Try looking in /proc/net for directories with the name of your driver module. It should have an eth0 file in it (or eth1 for the second detected card).
To find out why the other card is not detected try looking at the output of "dmesg". You should also check as suggested wether the module was compiled with your kernel (perhaps you forgot to activate the one for the old card when recompiling).
If it is an on-board NIC you might also want to check the BIOS. Perhaps the on-board devices are automatically deactivated when a card of the same function is detected (though I only really heard of that for sound and video where having two doesn't make much sense).