WSUS 3.0 on a Server 2003 machine. Fixed about 10 clients last week and about 40 today with this problem.  Denied the installation for now until I find out WHY this is happening. Possibly becaues of my AV running on the clients. I'm not sure. Here is how I fixed it:

01. Reboot your computer and while it's starting up tap F8 right after inital post.

02. When the menu show up, select the first option: "Repair Your Computer" 

03. In the new window click Command Prompt at the bottom.

04. If you are already in a system32 folder just enter "notepad.exe" otherwise type this and press enter: %windir%\system32\notepad.exe

05. Notepad will open. In notepad go to File-->Open.

06. Change the type of files notepad views from .txt to All Files (see pic)

07. Now in Notepad, go to C:\Windows\winsxs\ (or whichever drive Windows is installed on)

08. In that folder, find pending.xml and make a copy of it (ctrl + C then Ctrl + V)

09. Now open the original pending.xml (it will load really slow because the file is huge)

10. Press CNTRL+F and search for the following exactly: 0000000000000000.cdf-ms

---> That's 16 0's !

11. Delete the following text (yours might be a little different):

<Checkpoint/>

<DeleteFile path="\SystemRoot\WinSxS\FileMaps\_0000000000000000.cdf-ms"/>

<MoveFile source="\SystemRoot\WinSxS\Temp\PendingRenames\e56db1db48d4cb0199440000b01de419._0000000000000000.cdf-ms" destination="\SystemRoot\WinSxS\FileMaps\_0000000000000000.cdf-ms"/>

Your PC might not have all 3 sections of code (<Checkpoint>, <DeleteFile>, <MoveFile>). Just make sure you delete section "Checkpoint" and whatever other sections have "000000000000000.cdf-ms". They will be right next to each other.  

12. Reboot and make sure to watch to "start windows normally".