I read this thread last night before I allowed Software Update to install 10.6.8. After the install and reboot, my wallpapers on both monitors were unchanged.
After I posted this thread I did some mucking about and I think my problem was with the fact I'd moved my wallpaper out of it's original folder, so after I installed the update and it was configuring everything again, it couldn't find the image anymore.
I went into System Preferences and set the same wallpaper again and have not noticed any issue since.
Do you move your wallpapers out of their original directories after setting them prior to updating OS X? I'd be interested to know if that's the real issue.