It could really be caused by any number of things. What services are they running? Are they connected to the internet? What ports do they have open? What ports are supposed to be open?
Hopefully when you built these machines, you noted or you know now what ports are supposed to be open. Take a look at 'netstat -na' and see what ports are actually open. Granted if you did get compromised, these may not show up, so port scan your servers and see if they see any rogue servers.
As far as I know, most of the common DOS agents work on Win2k also. You are going to have to do some serious recon work on these servers. Note the open ports, the running services, server load and where that load is coming from.
If this doesn't point you in the right direction, give us some more details to try and isolate the problem a bit. Have you tried to capture any of the packets to see where they were destined for, seen if there is any other rogue traffic on your net (ie at a relatively quiet time sniff you net and see if there are any servers trying to connect to you or anything inside trying to connect to something out of the ordinary on the outside (ie an IRC server, as is common for DDOS clients.)
Hope this helps,
Paul