Windows 2000 DNS Problem

I was called to a small (two computer) network running 2000PRO on one and Win98 on the other. Internet connection is local cable through a switch. Win98 machine connects perfectly. Win2000 connects every other time. Reboot allows connection, but next reboot does not. System was loaded with Nimda, Nimda.D, Weird.10240 viruses which seem to be cleaned now. Discovered keystroke memorizing executables on the root directory (which I renamed and moved to another directory).

Any suggestions asto what files may have been damaged that would still affect the TCP/IP WAN connection so that it would work perfectly on 50% of the boots and not at all on the other 50%?