It changes the active partition after installation. For example, I had windows XP installed on sda1 and sda1 used to be the active partition. Then after I installed fedora on sda2, sda2 becomes the active partition. It didn't ask if you want to do that during the installation. I found this out because it cost me a lot of time to figure out the issue after a crashed install of fedora, after which my computer doesn't boot from HD any more.