I assume that what the guy at the genius bar did is an "archive and install" of OS X 10.4.8. As well as installing a new System Folder and applications while preserving your user folders, this would have created a "Previous System" folder on the root level of the hard drive which would have contained a few older versions of Apple applications that were updated by the new 10.4.8 install, and the old System Library folders. Hence the apparent duplication of the applications. The reason this happens is so that you can recover any applications that weren't preserved during the archive and install, should you need to. If things are working fine after a few days, then you can delete the Previous System folder to get rid of it.