samba - May 2010 - Problems with accessing samba share in Windows 2008R2 domain

Hi,

After upgrading the Windows DCs from Windows 2003R2 to Windows 2008R, 
the domain functional level was raised from Windows 2000 to Windows 
2008R2. As a consequence of this action, I found that a Application 
Management GPO no longer worked pushing applications to the companies 
desktops.

After some tweaking I found out in one MS document that a Windows 2008R2 
domain can not authenticate a Windows NT server as part of the GPO 
Application Software installation so the installation can not take 
place.  Copying the software to from the Samba hosted server to a 
Windows 2008R2 server and the installations took place without a problem.

Has anyone else come up against this problem, and is there a way round 
it as I would like to continue to use the Samba server?

Am I correct in assuming that Samba v3.x appears as a Windows NT server 
and Samba v4 as a Windows 2000/2003 server?