2nd post in a series of posts about Ngen Patch which slows down your machine during an update (and perhaps after for several minutes), but should leave everything fine afterwards.
Some more details: During install of the .Net Framework, many DLLs are placed in the GAC (Global assembly cache) and then during the install, most of them are NGENed, which means that a Native Image dll is created that can be run much faster than the DLLs that have been installed initially. This optimization takes several minutes (depending on the speed of your CPU and disk) and uses CPU and disk resources.
When a DLL is patched, other DLLs that depend on that DLL need to be re-NGENed. .Net 1.1 and .Net 2.0 are different in how they NGEN. .Net 1.1 NGENs syncronously and .Net 2.0 has an NGEN service which can NGEN over time.