As you probably know a CIFS user's access to a file/folder is the most restrictive combination of the CIFS share's permissions for that user or his/her groups, and the file/folder level permissions. In Windows those are your NTFS permissions, in Isilon they are implemented using extended ACLs which mimic the NTFS permissions.

Here's what you should do.

1. For the share, allow the "run as root" permission to a Windows account you have control over. Also make sure the share level permissions are correct for the users, e.g. if the user requires writing a file don't give them or their group a read-only share permission.

2. Unmount/remount the share as the account you used in #1. You should be able to do anything you want in the share regardless of filesystem permissions because now you are considered root

3. Using Windows open the folder's properties, in the security tab remove all the ACLs currently in there and create the permissions you want the folder to have.

4. When done remove the run as root permission from the share

5. User access to the share should work as expected.

Edit: I don't like the "Use Default ACLs" option for creating an SMB share. Just use the method above for setting permissions manually, there is much less room for error.