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Samba share, creating a file through Win gives wrong permissions

Having an issue that is racking my brain. I have searched and cannot find the answer (perhaps I'm not wording it correctly).

We have 2 Linux machines (RHEL 5, 2.6.18-348-4.1.el5xen) setup with Samba and a couple other pieces of software.

Samba works fine, except for the following
When a Windows user creates a file, the permissions include DOMAIN\USERNAME. If the same user creates that file under his Linux logon its just his USERNAME. This is an issue because our users can only create these files under Windows but the software we have under Linux only recognizes their Linux accounts. Before the Samba upgrade (see below) the Windows users files had just their USERNAMES listed under linux so it was "seamless"

Code:

-rw-r--r-- 1 user1        group01      0 Jun 18 14:11 FromLinuxFileBrowser.txt

-rwxrwxr-- 1 DOMAIN\user1  group01      0 Jun 18 14:10 FromWindowsExplorer.txt

Even the actual permissions are different. This wasn't an issue before we upgraded from Samba 3.0.33 to 3.0.8 (Because we're running a 2008r2 AD)

Any help would be greatly appreciated.

Well I can't say I have played with a new version of Samba for a while, but the first question that would dawn on me is to check the config files and see if any alterations were made as part of the upgrade?

Compared my new and old smb.conf and they are the same.

Also try ls -nl for those files, to see the actual uid and gid numbers instead of names.

Yes, its a completely different UID also. The gid is the same though (I do have a 'force group' option in the smb.conf