Are you attempting to publish via the Shavlik Patch plugin within SCCM or via SCUP?
Would it be possible for you to send in the AutoPublish.log or Update Publisher.log (SCUP.log)?
Thanks Adam, I did find the problem, the distribution points were set to enable prestaged content, and thus, were not downloading updates properly. Once again, hours of my life gone because of a checkbox. I'm not the only guy in the system, so it's hard to say how this came about.
Thanks again for the response.
Good to see you found the problem, and thanks for posting what caused it.