Erratic Win2K PDC & Linux DNS server Duo

Previously, I setup the DNS services of our Windows 2000 server (Our PDC) to resolve erratic DNS service provided by a third party software. I setup it up a way it was recommended by Microsoft.

But previously, one of my co-system administrator shut down the DNS service from the PDC and transferred the DNS service to a Linux box.

What’s happening now is that our end-users have a long time logging in to the network and they have reoccuring instances of being disconnected from the PDC and from other clients. And most of the time, they are asked for username and password to access other computers.

All these unlikely behavior were not experienced before. What seems to be the problem with such setup?