Here it is:
Mac OS X: About the Archive and Install feature
Basically, when you buy a new hard drive and want to migrate verything off your old drive to your new one you usually clone it. This is done using an app such as SuperDuper.
This works great - however when it rewrites the OS to the new drive it doesnt necessarily put everything back in the same location [mainly boot up files] so there is a noticeable lag when booting up when using your cloned drive.
The only way to cure this is to archive and install.
This basically moves your old OS to a folder called previous system, it saves all your applications, files, and settings so you do not loose them - it then installs a fresh version of your OS fixing the boot up problem.