When you attempt to install SBS 2008 UR 3 (969121) it may fail with error code 6BA "Windows Update encountered an unknown error". The C:\Windows\WindowsUpdate.log file for this update reports error 0x80070643 / 0x000006BA. Troubleshooting: One of the actions SBS2008 Update Rollup 3 (UR3) performs is to change the Integrated Windows authentication in the companyweb site from NTLM to Negotiate (Kerberos) while maintaining client integration to allow you to browse http://companyweb from the server after installing IE rollup 963027 or later, IE8 or Windows 2008 SP 2. Check the C:\Windows\temp\EnableKerberosLog_2009_<date_time>.log file for more clues.
Full Article: SBS blog