Force install updates on WSUS server
Solution 1:
i'm using the script already mentioned by Oskar with psexec to patch a bunch of servers. if a server has a borked WU Agent i use this script:
net stop bits
net stop wuauserv
reg delete HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate /f
rd /s /q %WINDIR%\SoftwareDistribution
gpupdate /force
wuauclt /resetauthorization /detectnow
Solution 2:
Perhaps the script attached to the first post on the link to this forum can resolve the problem:
Force installation of WSUS or Windows Updates
(I'm afraid you have to register in order to download the files.)
If you are interested in a more sophisticated solution, you could take a look at the Eminentware Extension Pack for WSUS (not free).
Solution 3:
In line with Oskar's solution. I've written a more comprehensive WUA script which can be used to force updates on client systems.