You may find slow down in system booting time after installing .NET Framework 4 client profile on a system and removing .NET Framework 4.0 client profile may resolve the issue. First you should check if there is an mscorsvw process that is taking a bunch of the CPU time. That would suggest that the slow down is related to contention with the ngen service. Running ngen /executequeueditems for both Framework and Framework64 folders and then seeing if the boot time issue resolves would also help narrow it to an issue with ngen competing for resources. The ngen service does try to ngen assemblies in the background until all the assemblies are ngen’d.