Method one in the below article resolved this issue for me. Seems to happen on DELL’s a fair bit.

This is related to KB article KB909639. http://support.microsoft.com/default.aspx?scid=kb;en-us;909639&sd=rss&spid=3208

SYMPTOMS
Consider the following scenario. You perform a recovery or migration of Microsoft Windows Small Business Server 2003 (Windows SBS). Then, you try to join an existing domain, as described in the following Microsoft Knowledge Base article:
884453 (http://support.microsoft.com/kb/884453 ) How to install Small Business Server 2003 in an existing Active Directory domain
When you run an integrated setup in this scenario, you receive an error message that is similar to the following, where Domain_name.local is the name of the local domain:
This server has a trust relationship with Domain_name.local.
This problem occurs when the following conditions are true:
• The original Windows SBS installation was preinstalled by an OEM.
• The domain on which Windows SBS is installed has a second domain controller.
Note Windows SBS does not support trusts. This article applies only if the error references your own domain and if that domain was originally preinstalled by the OEM.

CAUSE
This problem occurs because one of the domain GUIDs in the registry for Windows SBS is incorrectly referenced as part of the Windows SBS preinstallation process.

RESOLUTION
To resolve this problem, contact Microsoft Product Support Services.

As you can guess I called Microsoft. After being on hold for a while I went to my plan B and was able to resolve the original server issues.

But the resolution for the issues was answered today after I called MS and they gave me the answer to the issue.

Method 1: Bypass the trust check
1. Start the Windows SBS integrated setup process from the Windows SBS CD-ROM.
2. Cancel the setup process.
3. Locate the Sit xxxx .tmp folder in the system temp folder (%temp%).
Note The xxxx http://www.smallbizserver.net/Articles/tabid/ represents a random number that is generated by Setup.
4. In the Sit xxxx .tmp folder, use Notepad to open the Setup.sdb file.
5. In the Setup.sdb file, comment the trust check line by typing a semicolon at the start of the line.
6. Save the file, and then quit Notepad.
7. Restart the Windows SBS integrated setup process from the Sit xxxx .tmp folder.

Method 2: Change the GUID on the replica domain controllers
1. Change the permissions for the SECURITY hive. To do this, follow these steps:
a. Start Registry Editor, and then expand HKEY_LOCAL_MACHINE.
b. Under HKEY_LOCAL_MACHINE, right-click SECURITY, and then click Permissions.
c. Under Group or User Names, click Administrators. Under Permissions for Administrators, click to select the Allow check box in the Full Control row, and then click OK.
d. Quit Registry Editor.

2. Find the Active Directory domain GUID. To do this, follow these steps:
a. On a domain controller on which the Windows Support Tools component is installed, open a command prompt.
b. Change to the following directory: Drive_letter \Program Files\Support Tools
c. At the command prompt, type nltest/domain_trusts/all_trusts/v , and then press ENTER.
d. From the output, record the domain GUID string. You can locate the domain GUID string in the line of output that starts with “Dom Guid.” For example, the domain GUID string may appear as follows:
Dom Guid: 12345678-ABCD-EFGH-IJKL-MNOPQRSTUVWX
e. In this example, record the registry entry as follows:
78 56 34 12 CD AB GH EF IJ KL MN OP QR ST UV WX
f. Close the Command Prompt window.

3.
On each domain controller, change the value of the following registry entry to the value that you recorded in step 2e:
HKEY_LOCAL_MACHINE\SECURITY\Policy\PolDnDmG

Important You must change this registry entry on all domain controllers. Make a system state backup of all computers on which you will make this registry change. Verify that you have working backups. You must also restart all domain controllers, member servers, and workstations after you make this registry change. Additionally, you must restart the member servers and the workstations to receive the LSA GUID.

4. In Registry Editor, change the permissions on the SECURITY hive back to their original settings.

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