Current .NET Framework patches may not NGEN some assemblies as was recently discovered for KB928365. We have worked out a solution and Surupa Biswas, a PM on the CLR team, wanted me to pass along the following information.
As indicated in this post, an update to the CLR or to just the Framework 2.0 assemblies can leave applications based on Framework 3.0 sluggish for a while (until the machine is idle for more than 5 minutes and the NGen Service can pre-compile the Framework 3.0 assemblies whose dependencies were updated). We’re addressing this performance issue in the next CLR 2.0 update delivered with .NET Framework 3.5. We will ensure that future updates made to the CLR and/or Framework 2.0 assemblies will aggressively compile all critical framework assemblies (including WPF ones). Please note however that this change will only be effective for updates shipped post .NET Framework 3.5.