DNS Trouble

Hello,
I have inherited a win 2000 network environment, we have two linux DNS servers that are serving dual purpose, external and internal.
The problem that I have is with the windows dns system, it seems that its fighting with linux over primary DC control. I recently migrated groupwise to exchange 07. Now when running the client setup for mailboxes it either doesn’t see the active directory or it will get the username automatically, and then prompt for the password which is a eternal loop.

When I ping the domain it returns the wrong pdc. I’ve removed all the (NS) references to the server that is returned but it still returns the same server after the changes. Any ideas?