The more I read this original question, the more I keep thinking that there is likely to be a low-level answer to the problem. I am not so sure anymore, especially given all that you've tried so far :).
 
Being that as it may, I would like to fly this low-level kite anyway, in the hope that it may help.
 
So, you upgd the BDC - what happened to the original PDC thereafter? I am sorry if you've mentioned this in subsequent response, I just didn't see it.
 
Now, if you read Chapter 8 of the domain Migration Cookbook (http://www.microsoft.com/technet/treeview/default.asp?url=""> ), you will notice that the PDC is the one that ought to be up'ed, not the BDC. However, more importantly, note the pertinent information about potential REPLICATION (LMRepl) failure/problem IF some specific config are not made:
 

Synchronize File Replication Services

The two file replication services, LMRepl for Windows NT 4.0 and NT File Replication service (NTFRS) for the SYSVOL on Windows 2000, are not compatible, meaning they do not replicate files between them. Therefore, administrators have to create a manual process that copies new scripts from the logon folder in the SYSVOL to the LMRepl export folder on the Windows NT 4.0 domain controller.

The easiest way to perform this operation is as follows:  <Read full text on the link, it is midway down to the bottom of the page>

Also note:

  • Windows 2000 domain controllers do not replicate files using the LMRepl file replication service to Windows NT 4.0 domain controllers.

    Configure LMRepl File Replication Service

    Because the PDC won't be able to play the role as LMRepl export server after the operating system upgrade, another computer must be configured to play this role until all Windows NT 4.0 domain controllers have disappeared from the domain. Ideally, this should be the last Windows NT 4.0 domain controller that will be upgraded or decommissioned.

    There is more to that. Please take the time to read it. I honestly hope it helps narrow down the source of the problem.

  •  
     
     
    Sincerely,

    D�j� Ak�m�l�f�, MCSE MCSA MCP+I
    www.akomolafe.com
    www.iyaburo.com
    Do you now realize that Today is the Tomorrow you were worried about Yesterday?  -anon


    From: Rittenhouse, Cindy
    Sent: Fri 8/29/2003 7:32 AM
    To: [EMAIL PROTECTED]
    Subject: [ActiveDir] sysvol not replicating

    Two days ago a consulting firm upgraded a BDC at a remote location to
    Windows 2000. After the upgrade users had all types of trouble connecting.
    It seems the sysvol is not replicating because the
    Do_Not_Remove_NtFrs_PreInstall_Directory, Policies directory, and Scripts
    directory do not exist on the remote server in either the sysvol\domain or
    the sysvol\sysvol directory. The rest of AD seems to be replicating fine.
    Can I simply copy those directories from one of my DCs to the DC in the
    remote location?
    Thanks
    
    Cynthia Rittenhouse  MCSE,CCNA
    LAN Administrator
    County of Lancaster
    Lancaster, PA 17602
    
    
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