My organization was hit with this also. One easy solution I found for pinpointing infected PCs was by using Etherreal, a packet level sniffing utility that is free. Install this on a patched PC (with all RPC patches) and then install the program along with winpcap (it is needed to run Etherreal). Once you get everything installed, slap a hub into the network somewhere or setup a mirrored port if you have switches. I simply ran our Internet pipe through a hub and then onto our core switch with this PC also hanging off the hub. Once all of this is done and you have network connectivity on the PC run Etherreal and setup an ICMP filter (this filters only on ICMP traffic, the way that Nachi spreads itself in a network). Ethereal provides you the source and destination IP addresses, the time of the ping attempt and some other stuff. You are looking for multiple icmp requests from the same source IP address to several different IP addressess (these destination IP addresses will show up in ascending order, it's not hard to see where your culprit(s) are. Once you find them, connect to the PC and disable the WINS service (it's bogus) and apply all patches as recommended by Microsoft (LOL). This will help you get your infection under control.
Hope this helps.