Rob Eisenberg recently posted that he was experiencing performance issues related to recent Windows auto updates that he received. The issue was caused by a .NET Framework security update on 7/10.
From the information I have it appears that a significant number of assemblies are being ngen'd after reboot. The NGEN'ing itself can use a significant number of CPU cycles but if you happen to be running .NET applications before the NGEN'ing completes you'll likely see the results of JIT'ing as well. The overall experience can be very poor performance. Once NGEN'ing is complete, though, the problem shouldn't continue. The right people are looking into the issue now; if/when I've got new info I'll post.