2000 pdc died 2003 now running, just not right.

So win2000, our PDC died, and I had a new DC in place already when it happened.  (DCwin2003) is the name for future reference.

Adding dcwin2003 to the domain was a very straight forward process, I did a lot of reading to make sure it would go smooth and it really did, I did the adprep /forestpresp and /domainprep and no errors at all.  

For the first few days of the DC running everything was fine, but then when win2000 died, (which was our main file server as well), is when I started noticing problems.  

Our files are now on dcwin2003 and thus all of my users logon scripts had to be changed to reflect the new file location, the scripts are simply not running.  I've created test scripts with popup dialog boxes and they simply do not run at all on login.  When running them locally everything works fine.

Another issue I noticed is that when creating a new user, I get warned that the GCS cannot be found, I tried resolving this by manually setting dcveto as the GCS, but not sure if that change took place.

This is also causing "some" of my users to not be able to authenticate to servers that aren't dc's.  I have yet to figure out the pattern of users that can/cannot authenticate, but it has to be DC/GCS related.