12.04 is not final yet and since the release of Beta 2 over 3 weeks ago lots of packages got updated. I would not expect such a feature to work flawlessly in Beta state. Did you really upgrade from CD, not just reinstall?
In theory the installation media contains a repository of packages and the upgrade from installation media functionality works like the regular upgrade but prioritizes packages from the installation media. Obviously the CD only contains a very limited number of packages needed for the default install. The DVD contains a lot more packages, but not all. The upgrade should detect your selection of packages and replace them with newer ones. Packages not found locally should be downloaded if there is an Internet connection available. The upgrade should warn about PPAs, software that is going to be removed and replacement/alteration of configuration files if I recall correctly. In case of no Internet connection, the package should be removed/uninstalled but the configuration files shouldn't be altered.
That said upgrading from installation media and without installation media should be the same. As long as there are packages for your installed applications in the repository of the new release you're upgrading to nothing should be uninstalled. If you don't have an Internet connection at the time of upgrade and no local repository with the package for the new release, then of course no package can be found and the application will be uninstalled.