Hi.
First of all, i'll assume the problem is that a user logs on to a NT4 computer, then logs on to a windows 2000 computer, and then logs on to a nt4 computer and gets into trouble.
We have experienced the same thing, and the solution we selected was to remove the User profiles from user manager. this was by far the easiest and most cost effective.
The drawback is that user settings dont follow the users from computer to computer.
As for NT policies. They work in the same way for NT4 and for Windows 2000. That is the computer loads a .POL file when it boots from the netlogon share of the domain controller(default setup)
But, as soon as you trow Active Directory into the picture you get a problem.
NT 4 dont care about AD, it still works the same way.
But WIndows 2000/XP will start using GPO instead of .POL files as soon it detects AD( you can not disable this feature, this possibility was removed after Windows 2000 Beta)
Even if the Windows 2000 computer is in a NT4 resource domain, as soon as a AD user account logs on, it will use GPO instead of .POL for the user part of the policy.
That means you will have to duplicate the settings in the .POL file you are using, and apply them with both .POL and with GPO.
Remember, its not a bug, its a feature:))