I have configured net.if.discovery on my Windows 2003 server. The agents is reporting TWO nics with the same name. However, on this server, the two NICs are reported as
Broadcom NetXtreme Gigabit Ethernet
and
Broadcom NetXtreme Gigabit Ethernet#1

The command (from my Zabbix Server)
#zabbix_get -s myserver -k net.if.in.discovery

Returns
{
"data":[
{
"

{#IFNAME}":"Broadcom NetXtreme Gigabit Ethernet"},
{
"{#IFNAME}

":"Broadcom NetXtreme Gigabit Ethernet"},
{
"

{#IFNAME}":"MS TCP Loopback interface"}]}

(excerpt from zabbix_agentd.log below)
6964:20120522:062527.151 Processing request.
6964:20120522:062527.151 Requested [net.if.discovery]
6964:20120522:062527.151 Sending back [{
"data":[
{
"{#IFNAME}

":"Broadcom NetXtreme Gigabit Ethernet"},
{
"

{#IFNAME}":"Broadcom NetXtreme Gigabit Ethernet"},
{
"{#IFNAME}

":"MS TCP Loopback interface"}]}]
(snip)

If you need any more info, just shout. I will be AFK for most of today and tomorrow, though.