Up until 1.0.4 you had to choose whether to perform a fresh install or a semi manual upgrade. The patch files are for the upgrade but contain exactly the same version as the full install, just in a directory structure that can be amnually copied over an existing FB install.
This changes dramatically with 1.0.5 and all future releases. There will be 1 and only 1 package that performs both fresh installs as well as upgrades. See more details here:
www.bestofjoomla.com/component/option,co...w/id,54379/catid,78/