Contributed By: Mohammed. Athif Khaleel [MVP SUS/ WSUS]
This is actually normal with V5 version of Windows Update.  That said, it means,

C:\Windows\Windows Update.log refers to V4

C:\Windows\WindowsUpdate.log refers to V5

I feel, C:\Windows\WindowsUpdate.log (without the space) refers to V5 and is designed for WUS; though, both the log files are compatible with SUS.  Two Windows Update Log files with V5 component installed is actually normal.

Also, make sure the following registry values exist. If they don't create them.

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate\Auto Update]

"SusServerVersion" = REG_DWORD: 0x00000001 (1)

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate\Auto Update]

"ConfigVer" = REG_DWORD: 0x00000001 (1)

***NOTE: If these values are not present, a v5 client tends to update from WindowsUpdate rather than SUS.

In my workstation, it looks something like:

C:\Documents and Settings\User>Reg query "HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate\Auto Update"

! REG.EXE VERSION 3.0

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate\AutoUpdate

    SusServerVersion    REG_DWORD      0x1
    AUState    REG_DWORD      0x2
    NextDetectionTime REG_SZ 2004-10-06 05:54:40
    ConfigVer REG_DWORD      0x1
    LastWaitTimeout    REG_SZ 2004.10.07 01:23:20

Happy Testing!
Athif
Mohammed. Athif Khaleel
"Save the Internet. Keep all Systems Patched"