Hello!
Since this is my first post here I want to say thank you for your brilliant soft that makes life easier.
As I stated in subject WSUSOU is not installing some updates that were already downloaded by it. I've tested your latest version which is v10.9.1 on a fresh installed Win7 x64 Ultimate on VirtualBox. Connection to internet was disabled, WU set to never check for updates. I've tested it three times. First time access to all update files from WSUSOU were from network resource. It looked like everything is fine but missing updates were listed in WU history as failed and they were not present on Installed Updates list.
I thought the problem was lack of access to network resource so I made another clean install of W7. This time i unpacked all required files to 'hard drive'. It completed installation of 144 updates (just like last time except requirements for IE, etc) but this time there were only 11 updates listed in WU history and all succesful and there were no previosly failed and missing updates on that list.
Third time i tested it again was with fully destroying all WSUSUO files and downloading them again. The outcome was the same.
I'm posting you logs that might tell you something more about this.