I am very interested in a resolution to this. I have seen exactly this behaviour.
I have tried changing the ownership of the shares on my samba server to use the domain
administrator and group to domain admins. Then I am able to set ACL's on windows and
they seem to get set. I can change share ownership, folder ownership and give users full
control of folders. However despite the ACL's seemingly being set in windows they are
never actually set at the file system level.